3MKC | pdb_00003mkc

Crystal structure of a putative racemase

• PDB DOI: https://doi.org/10.2210/pdb3MKC/pdb

• Classification: ISOMERASE
• Organism(s): Pseudovibrio sp. JE062
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-04-14 Released: 2010-04-28 
• Deposition Author(s): Eswaramoorthy, S., 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: 1.77 Å
• R-Value Free: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Literature

Crystal structure of a putative racemase

Eswaramoorthy, S., Burley, S.K., Swaminathan, S.

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: 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 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.44 kDa 
• Atom Count: 3,115 
• Modeled Residue Count: 380 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
racemase	A	394	Pseudovibrio sp. JE062	Mutation(s): 0  Gene Names: PJE062_745

Small Molecules

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: 1.77 Å
• R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.838	α = 90
b = 134.838	β = 90
c = 94.323	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELX	model building
SHARP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-28 
Deposition Author(s): Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-04-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Structure summary