3CQY | pdb_00003cqy

Crystal structure of a functionally unknown protein (SO_1313) from Shewanella oneidensis MR-1

• PDB DOI: https://doi.org/10.2210/pdb3CQY/pdb

• Classification: TRANSFERASE
• Organism(s): Shewanella oneidensis MR-1
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2008-04-03 Released: 2008-04-22 
• Deposition Author(s): Tan, K., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.211 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

The structure of a functionally unknown protein (SO_1313) from Shewanella oneidensis MR-1.

Tan, K., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A.M., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 80.82 kDa 
• Atom Count: 6,096 
• Modeled Residue Count: 739 
• Deposited Residue Count: 740 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anhydro-N-acetylmuramic acid kinase	A, B	370	Shewanella oneidensis MR-1	Mutation(s): 0  Gene Names: NP_716933, anmK, SO_1313 EC: 2.7.1 (PDB Primary Data), 2.7.1.170 (UniProt)
UniProt
Find proteins for Q8EHB5 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8EHB5  Go to UniProtKB:  Q8EHB5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN	F [auth A], G [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A], H [auth B], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-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: 2.30 Å
• R-Value Free:  0.211 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.816	α = 90
b = 147.816	β = 90
c = 117.687	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-22 
Deposition Author(s): Tan, K., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-04-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary