3GIR | pdb_00003gir

Crystal structure of glycine cleavage system aminomethyltransferase T from Bartonella henselae

PDB DOI: https://doi.org/10.2210/pdb3GIR/pdb

Classification: TRANSFERASE
Organism(s): Bartonella henselae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-06 Released: 2009-03-17
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.205 (Depositor), 0.216 (DCC)
R-Value Work:
0.175 (Depositor), 0.187 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of glycine cleavage system aminomethyltransferase T from Bartonella henselae

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 42.91 kDa
Atom Count: 3,355
Modeled Residue Count: 361
Deposited Residue Count: 393
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminomethyltransferase	A	393	Bartonella henselae	Mutation(s): 0 Gene Names: gcvT, BH12840 EC: 2.1.2.10
UniProt
Find proteins for A0A0H3M6H9 (Bartonella henselae (strain ATCC 49882 / DSM 28221 / CCUG 30454 / Houston 1)) Explore A0A0H3M6H9 Go to UniProtKB: A0A0H3M6H9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3M6H9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.205 (Depositor), 0.216 (DCC)
R-Value Work: 0.175 (Depositor), 0.187 (DCC)
R-Value Observed: 0.176 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.98	α = 90
b = 72.67	β = 90
c = 138.02	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-03-17

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2009-03-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.