3MBO | pdb_00003mbo

Crystal Structure of the Glycosyltransferase BaBshA bound with UDP and L-malate

PDB DOI: https://doi.org/10.2210/pdb3MBO/pdb

Classification: TRANSFERASE
Organism(s): Bacillus anthracis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-03-25 Released: 2010-09-29
Deposition Author(s): Wallace, B.D., Claiborne, A., Redinbo, M.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.31 Å
R-Value Free:
0.257 (Depositor), 0.255 (DCC)
R-Value Work:
0.228 (Depositor), 0.226 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Characterization of the N-Acetyl-alpha-d-glucosaminyl l-Malate Synthase and Deacetylase Functions for Bacillithiol Biosynthesis in Bacillus anthracis

Parsonage, D., Newton, G.L., Holder, R.C., Wallace, B.D., Paige, C., Dos Santos, P.C., Redinbo, M.R., Fahey, R.C., Reid, S.D., Claiborne, A.

(2010) Biochemistry 49: 8398

Macromolecule Content

Total Structure Weight: 375.03 kDa
Atom Count: 23,880
Modeled Residue Count: 2,961
Deposited Residue Count: 3,312
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase, group 1 family	A, B, C, D, E A, B, C, D, E, F, G, H	414	Bacillus anthracis	Mutation(s): 0 Gene Names: BaBshA, BAS1445, BA_1558, GBAA1558, GBAA_1558 EC: 2.4.1
UniProt
Find proteins for Q81ST7 (Bacillus anthracis) Explore Q81ST7 Go to UniProtKB: Q81ST7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q81ST7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain KA [auth H] SDF format, chain R [auth C] SDF format, chain Z [auth E] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain R [auth C] MOL2 format, chain Z [auth E] mmCIF format, chain I [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain R [auth C] mmCIF format, chain Z [auth E]	I [auth A], KA [auth H], R [auth C], Z [auth E]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain I [auth A] Focus chain KA [auth H] Focus chain R [auth C] Focus chain Z [auth E] Interactions & Density Focus chain I [auth A] Focus chain KA [auth H] Focus chain R [auth C] Focus chain Z [auth E]
MLT Query on MLT Download:Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain MA [auth H] SDF format, chain O [auth A] SDF format, chain U [auth C] MOL2 format, chain EA [auth E] MOL2 format, chain MA [auth H] MOL2 format, chain O [auth A] MOL2 format, chain U [auth C] mmCIF format, chain EA [auth E] mmCIF format, chain MA [auth H] mmCIF format, chain O [auth A] mmCIF format, chain U [auth C]	EA [auth E], MA [auth H], O [auth A], U [auth C]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain EA [auth E] Focus chain MA [auth H] Focus chain O [auth A] Focus chain U [auth C] Interactions & Density Focus chain EA [auth E] Focus chain MA [auth H] Focus chain O [auth A] Focus chain U [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain J [auth A] SDF format, chain JA [auth F] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth H] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain BA [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain BA [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain HA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain BA [auth E]	AA [auth E] BA [auth E] CA [auth E] DA [auth E] GA [auth F] AA [auth E], BA [auth E], CA [auth E], DA [auth E], GA [auth F], HA [auth F], IA [auth F], J [auth A], JA [auth F], K [auth A], L [auth A], LA [auth H], M [auth A], N [auth A], P [auth B], Q [auth B], S [auth C], T [auth C], W [auth D], X [auth D], Y [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain V [auth C] MOL2 format, chain FA [auth E] MOL2 format, chain V [auth C] mmCIF format, chain FA [auth E] mmCIF format, chain V [auth C]	FA [auth E], V [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain FA [auth E] Focus chain V [auth C] Interactions & Density Focus chain FA [auth E] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.31 Å
R-Value Free: 0.257 (Depositor), 0.255 (DCC)
R-Value Work: 0.228 (Depositor), 0.226 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 226.266	α = 90
b = 226.266	β = 90
c = 75.354	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-09-29

Deposition Author(s):

Wallace, B.D.

Claiborne, A.

Redinbo, M.R.

Revision History (Full details and data files)

Version 1.0: 2010-09-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-06
Changes: Structure summary