3GBX | pdb_00003gbx

Serine hydroxymethyltransferase from Salmonella typhimurium

• PDB DOI: https://doi.org/10.2210/pdb3GBX/pdb

• Classification: TRANSFERASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-20 Released: 2009-03-10 
• Deposition Author(s): Osipiuk, J., Nocek, B., Zhou, M., Stam, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.191 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

X-ray crystal structure of serine hydroxymethyltransferase from Salmonella typhimurium.

Osipiuk, J., Nocek, B., Zhou, M., Stam, J., Anderson, W.F., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 92.84 kDa 
• Atom Count: 6,646 
• Modeled Residue Count: 773 
• Deposited Residue Count: 840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B	420	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: glyA, STM2555 EC: 2.1.2.1
UniProt
Find proteins for P0A2E1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A2E1  Go to UniProtKB:  P0A2E1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.191 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33gbx

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.955	α = 90
b = 49.734	β = 110.67
c = 94.736	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-10 
Deposition Author(s): Osipiuk, J., Nocek, B., Zhou, M., Stam, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary