2GHR | pdb_00002ghr

Crystal structure of homoserine o-succinyltransferase (NP_981826.1) from Bacillus cereus ATCC 10987 at 2.40 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2GHR/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus cereus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-03-27 Released: 2006-04-11 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 A resolution

Zubieta, C., Krishna, S.S., McMullan, D., Miller, M.D., Abdubek, P., Agarwalla, S., Ambing, E., Astakhova, T., Axelrod, H.L., Carlton, D., Chiu, H.J., Clayton, T., Deller, M., Didonato, M., Duan, L., Elsliger, M.A., Grzechnik, S.K., Hale, J., Hampton, E., Han, G.W., Haugen, J., Jaroszewski, L., Jin, K.K., Klock, H.E., Knuth, M.W., Koesema, E., Kumar, A., Marciano, D., Morse, A.T., Nigoghossian, E., Oommachen, S., Reyes, R., Rife, C.L., Bedem, H.V., Weekes, D., White, A., Xu, Q., Hodgson, K.O., Wooley, J., Deacon, A.M., Godzik, A., Lesley, S.A., Wilson, I.A.

(2007) Proteins 68: 999-1005

• PubMed: 17546672 
• DOI: https://doi.org/10.1002/prot.21208
• Primary Citation of Related Structures:  
  2GHR

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Organizational Affiliation: 
• Joint Center for Structural Genomics, Stanford University, Menlo Park, California, USA.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 35.82 kDa 
• Atom Count: 2,293 
• Modeled Residue Count: 269 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine O-succinyltransferase	A	302	Bacillus cereus	Mutation(s): 6  Gene Names: metA EC: 2.3.1.46 (PDB Primary Data), 2.3.1.31 (UniProt)
UniProt
Find proteins for Q72X44 (Bacillus cereus (strain ATCC 10987 / NRS 248)) Explore Q72X44  Go to UniProtKB:  Q72X44

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32GHR

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.89	α = 90
b = 95.89	β = 90
c = 75.403	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-11 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-04-11
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Advisory, Database references, Derived calculations
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary