3CK5

Crystal structure of a racemase from Streptomyces coelicolor A3(2) with bound magnesium

• PDB DOI: https://doi.org/10.2210/pdb3CK5/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces coelicolor A3(2)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-14 Released: 2008-03-25 
• Deposition Author(s): Rao, K.N., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.264 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 

Starting Model: experimental

Literature

Crystal structure of a racemase from Streptomyces coelicolor A3(2) with bound magnesium.

Rao, K.N., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 164.93 kDa 
• Atom Count: 11,164 
• Modelled Residue Count: 1,405 
• Deposited Residue Count: 1,484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative racemase	A, B, C, D	371	Streptomyces coelicolor A3(2)	Mutation(s): 0  Gene Names: SCO3480, SCE65.16c EC: 5.5.1.25
UniProt
Find proteins for Q9RKF7 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9RKF7  Go to UniProtKB:  Q9RKF7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth B], G [auth C], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	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: 0.264 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.603	α = 90
b = 177.603	β = 90
c = 112.06	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Rao, K.N., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection