5V0T | pdb_00005v0t

Crystal structure of an alpha,alpha-trehalose-phosphate synthase (UDP-forming) from Burkholderia xenovorans in complex with glucose-6-phosphate

PDB DOI: https://doi.org/10.2210/pdb5V0T/pdb

Classification: TRANSFERASE
Organism(s): Paraburkholderia xenovorans LB400
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-02-28 Released: 2017-04-05
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.178 (Depositor), 0.180 (DCC)
R-Value Work:
0.155 (Depositor), 0.160 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of an alpha,alpha-trehalose-phosphate synthase (UDP-forming) from Burkholderia xenovorans in complex with glucose-6-phosphate

Mayclin, S.J., Dranow, D.M., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 450.42 kDa
Atom Count: 32,349
Modelled Residue Count: 3,628
Deposited Residue Count: 3,952
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha,alpha-trehalose-phosphate synthase (UDP-forming)	A, B, C, D, E A, B, C, D, E, F, G, H	494	Paraburkholderia xenovorans LB400	Mutation(s): 0 Gene Names: Bxe_A1242 EC: 2.4.1.15
UniProt
Find proteins for Q13W28 (Paraburkholderia xenovorans (strain LB400)) Explore Q13W28 Go to UniProtKB: Q13W28
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13W28
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download Ideal Coordinates CCD File SDF format, chain CC [auth H] SDF format, chain EB [auth E] SDF format, chain I [auth A] SDF format, chain MA [auth C] SDF format, chain PB [auth F] SDF format, chain UA [auth D] SDF format, chain V [auth B] SDF format, chain YB [auth G] MOL2 format, chain CC [auth H] MOL2 format, chain EB [auth E] MOL2 format, chain I [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain PB [auth F] MOL2 format, chain UA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain YB [auth G] mmCIF format, chain CC [auth H] mmCIF format, chain EB [auth E] mmCIF format, chain I [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain PB [auth F] mmCIF format, chain UA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain YB [auth G]	CC [auth H] EB [auth E] I [auth A] MA [auth C] PB [auth F] CC [auth H], EB [auth E], I [auth A], MA [auth C], PB [auth F], UA [auth D], V [auth B], YB [auth G]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain CC [auth H] Focus chain EB [auth E] Focus chain I [auth A] Focus chain MA [auth C] Focus chain PB [auth F] Focus chain UA [auth D] Focus chain V [auth B] Focus chain YB [auth G] Interactions & Density Focus chain CC [auth H] Focus chain EB [auth E] Focus chain I [auth A] Focus chain MA [auth C] Focus chain PB [auth F] Focus chain UA [auth D] Focus chain V [auth B] Focus chain YB [auth G]
G6P Query on G6P Download Ideal Coordinates CCD File SDF format, chain DC [auth H] SDF format, chain FB [auth E] SDF format, chain J [auth A] SDF format, chain NA [auth C] SDF format, chain QB [auth F] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain ZB [auth G] MOL2 format, chain DC [auth H] MOL2 format, chain FB [auth E] MOL2 format, chain J [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain QB [auth F] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain ZB [auth G] mmCIF format, chain DC [auth H] mmCIF format, chain FB [auth E] mmCIF format, chain J [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain QB [auth F] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain ZB [auth G]	DC [auth H] FB [auth E] J [auth A] NA [auth C] QB [auth F] DC [auth H], FB [auth E], J [auth A], NA [auth C], QB [auth F], VA [auth D], W [auth B], ZB [auth G]	6-O-phosphono-alpha-D-glucopyranose C₆ H₁₃ O₉ P NBSCHQHZLSJFNQ-DVKNGEFBSA-N		Interactions Focus chain DC [auth H] Focus chain FB [auth E] Focus chain J [auth A] Focus chain NA [auth C] Focus chain QB [auth F] Focus chain VA [auth D] Focus chain W [auth B] Focus chain ZB [auth G] Interactions & Density Focus chain DC [auth H] Focus chain FB [auth E] Focus chain J [auth A] Focus chain NA [auth C] Focus chain QB [auth F] Focus chain VA [auth D] Focus chain W [auth B] Focus chain ZB [auth G]
TAR Query on TAR Download Ideal Coordinates CCD File SDF format, chain GB [auth E] MOL2 format, chain GB [auth E] mmCIF format, chain GB [auth E]	GB [auth E]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain GB [auth E] Interactions & Density Focus chain GB [auth E]
OXD Query on OXD Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain JB [auth E] SDF format, chain O [auth A] SDF format, chain RA [auth C] SDF format, chain UB [auth F] MOL2 format, chain EA [auth B] MOL2 format, chain JB [auth E] MOL2 format, chain O [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain UB [auth F] mmCIF format, chain EA [auth B] mmCIF format, chain JB [auth E] mmCIF format, chain O [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain UB [auth F]	EA [auth B], JB [auth E], O [auth A], RA [auth C], UB [auth F]	OXALIC ACID C₂ H₂ O₄ MUBZPKHOEPUJKR-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain JB [auth E] Focus chain O [auth A] Focus chain RA [auth C] Focus chain UB [auth F] Interactions & Density Focus chain EA [auth B] Focus chain JB [auth E] Focus chain O [auth A] Focus chain RA [auth C] Focus chain UB [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AC [auth G] SDF format, chain EC [auth H] SDF format, chain FC [auth H] SDF format, chain HB [auth E] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain OA [auth C] SDF format, chain OB [auth E] SDF format, chain PA [auth C] SDF format, chain RB [auth F] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain Y [auth B] MOL2 format, chain AC [auth G] MOL2 format, chain EC [auth H] MOL2 format, chain FC [auth H] MOL2 format, chain HB [auth E] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain OA [auth C] MOL2 format, chain OB [auth E] MOL2 format, chain PA [auth C] MOL2 format, chain RB [auth F] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] mmCIF format, chain AC [auth G] mmCIF format, chain EC [auth H] mmCIF format, chain FC [auth H] mmCIF format, chain HB [auth E] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain OA [auth C] mmCIF format, chain OB [auth E] mmCIF format, chain PA [auth C] mmCIF format, chain RB [auth F] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain Y [auth B]	AC [auth G] EC [auth H] FC [auth H] HB [auth E] K [auth A] AC [auth G], EC [auth H], FC [auth H], HB [auth E], K [auth A], L [auth A], LA [auth B], OA [auth C], OB [auth E], PA [auth C], RB [auth F], WA [auth D], X [auth B], XA [auth D], Y [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AC [auth G] Focus chain EC [auth H] Focus chain FC [auth H] Focus chain HB [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth B] Focus chain OA [auth C] Focus chain OB [auth E] Focus chain PA [auth C] Focus chain RB [auth F] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Interactions & Density Focus chain AC [auth G] Focus chain EC [auth H] Focus chain FC [auth H] Focus chain HB [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth B] Focus chain OA [auth C] Focus chain OB [auth E] Focus chain PA [auth C] Focus chain RB [auth F] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain BC [auth G] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain GC [auth H] SDF format, chain IB [auth E] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain QA [auth C] SDF format, chain SB [auth F] SDF format, chain TB [auth F] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] SDF format, chain YA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain BC [auth G] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain GC [auth H] MOL2 format, chain IB [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain SB [auth F] MOL2 format, chain TB [auth F] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] MOL2 format, chain YA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain BC [auth G] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain GC [auth H] mmCIF format, chain IB [auth E] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain SB [auth F] mmCIF format, chain TB [auth F] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D] mmCIF format, chain YA [auth D]	AA [auth B] BA [auth B] BC [auth G] CA [auth B] DA [auth B] AA [auth B], BA [auth B], BC [auth G], CA [auth B], DA [auth B], GC [auth H], IB [auth E], M [auth A], N [auth A], QA [auth C], SB [auth F], TB [auth F], YA [auth D], Z [auth B], ZA [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain BC [auth G] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain GC [auth H] Focus chain IB [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain QA [auth C] Focus chain SB [auth F] Focus chain TB [auth F] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain BC [auth G] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain GC [auth H] Focus chain IB [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain QA [auth C] Focus chain SB [auth F] Focus chain TB [auth F] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain BB [auth D] SDF format, chain CB [auth D] SDF format, chain DB [auth D] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain HC [auth H] SDF format, chain IA [auth B] SDF format, chain IC [auth H] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain KB [auth E] SDF format, chain LB [auth E] SDF format, chain MB [auth E] SDF format, chain NB [auth E] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain SA [auth C] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain VB [auth F] SDF format, chain WB [auth F] SDF format, chain XB [auth F] SDF format, chain U [auth A] MOL2 format, chain AB [auth D] MOL2 format, chain BB [auth D] MOL2 format, chain CB [auth D] MOL2 format, chain DB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain HC [auth H] MOL2 format, chain IA [auth B] MOL2 format, chain IC [auth H] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth E] MOL2 format, chain LB [auth E] MOL2 format, chain MB [auth E] MOL2 format, chain NB [auth E] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain VB [auth F] MOL2 format, chain WB [auth F] MOL2 format, chain XB [auth F] MOL2 format, chain U [auth A] mmCIF format, chain AB [auth D] mmCIF format, chain BB [auth D] mmCIF format, chain CB [auth D] mmCIF format, chain DB [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain HC [auth H] mmCIF format, chain IA [auth B] mmCIF format, chain IC [auth H] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth E] mmCIF format, chain LB [auth E] mmCIF format, chain MB [auth E] mmCIF format, chain NB [auth E] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain VB [auth F] mmCIF format, chain WB [auth F] mmCIF format, chain XB [auth F] mmCIF format, chain U [auth A]	AB [auth D] BB [auth D] CB [auth D] DB [auth D] FA [auth B] AB [auth D], BB [auth D], CB [auth D], DB [auth D], FA [auth B], GA [auth B], HA [auth B], HC [auth H], IA [auth B], IC [auth H], JA [auth B], KA [auth B], KB [auth E], LB [auth E], MB [auth E], NB [auth E], P [auth A], Q [auth A], R [auth A], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], VB [auth F], WB [auth F], XB [auth F]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain HC [auth H] Focus chain IA [auth B] Focus chain IC [auth H] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain KB [auth E] Focus chain LB [auth E] Focus chain MB [auth E] Focus chain NB [auth E] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain VB [auth F] Focus chain WB [auth F] Focus chain XB [auth F] Interactions & Density Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain HC [auth H] Focus chain IA [auth B] Focus chain IC [auth H] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain KB [auth E] Focus chain LB [auth E] Focus chain MB [auth E] Focus chain NB [auth E] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain VB [auth F] Focus chain WB [auth F] Focus chain XB [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.178 (Depositor), 0.180 (DCC)
R-Value Work: 0.155 (Depositor), 0.160 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.92	α = 91.36
b = 105.95	β = 90.37
c = 135.71	γ = 89.97

Software Package:

Software Name	Purpose
XSCALE	data scaling
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-04-05

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-04-05
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary