5A4J | pdb_00005a4j

Crystal structure of FTHFS1 from T.acetoxydans Re1

PDB DOI: https://doi.org/10.2210/pdb5A4J/pdb

Classification: LIGASE
Organism(s): Tepidanaerobacter acetatoxydans Re1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-06-10 Released: 2016-07-06
Deposition Author(s): Bergdahl, R., Jacobson, F., Muller, B., Mikkelsen, N., Schurer, A., Sandgren, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.220 (Depositor), 0.202 (DCC)
R-Value Work:
0.184 (Depositor)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Characterization, Crystallization and Three- Dimensional Structures of Formyltetrahydrofolate Synthetase (Fthfs) from the Syntrophic Acetate Oxidising Bacterium Tepidanaerobacter Acetatoxydans Re1

Bergdahl, R., Jacobson, F., Muller, B., Mikkelsen, N., Schurer, A., Sandgren, M.

To be published.

Macromolecule Content

Total Structure Weight: 243.87 kDa
Atom Count: 18,075
Modeled Residue Count: 2,227
Deposited Residue Count: 2,236
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FORMATE--TETRAHYDROFOLATE LIGASE	A, B, C, D	559	Tepidanaerobacter acetatoxydans Re1	Mutation(s): 0 EC: 6.3.4.3
UniProt
Find proteins for K7SWE7 (Tepidanaerobacter acetatoxydans (strain DSM 21804 / JCM 16047 / Re1)) Explore K7SWE7 Go to UniProtKB: K7SWE7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K7SWE7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TAR Query on TAR Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain S [auth B] SDF format, chain I [auth A] MOL2 format, chain V [auth C] MOL2 format, chain S [auth B] MOL2 format, chain I [auth A] mmCIF format, chain V [auth C] mmCIF format, chain S [auth B] mmCIF format, chain I [auth A]	I [auth A], S [auth B], V [auth C]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain I [auth A] Focus chain S [auth B] Focus chain V [auth C] Interactions & Density Focus chain I [auth A] Focus chain S [auth B] Focus chain V [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain H [auth A]	H [auth A], Q [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain Q [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain W [auth C] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain W [auth C] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain W [auth C] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A], W [auth C], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain W [auth C] Focus chain Z [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] N [auth B] O [auth B] E [auth A], F [auth A], G [auth A], N [auth B], O [auth B], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain M [auth A] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain M [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain M [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] L [auth A] M [auth A] T [auth B] AA [auth D], BA [auth D], L [auth A], M [auth A], T [auth B], U [auth B], X [auth C], Y [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain X [auth C] Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.220 (Depositor), 0.202 (DCC)
R-Value Work: 0.184 (Depositor)
R-Value Observed: 0.186 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.038	α = 90
b = 100.98	β = 90
c = 258.05	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-07-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-07-06
Type: Initial release
Version 1.1: 2018-01-17
Changes: Data collection
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description