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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.205 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of glycine cleavage system aminomethyltransferase T from Bartonella henselae

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.205 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33GIR

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

Entry History 

Deposition Data

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

Revision History  

• 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