3NZG

Crystal structure of a putative racemase with Mg ion

• PDB DOI: https://doi.org/10.2210/pdb3NZG/pdb

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


• Deposited: 2010-07-16 Released: 2010-08-11 
• Deposition Author(s): Eswaramoorthy, S., Raparia, E., 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: 2.00 Å
• R-Value Free: 0.244 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 

Literature

Crystal structure of a putative racemase with Mg ion

Eswaramoorthy, S., Raparia, E., 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 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 178.42 kDa 
• Atom Count: 12,214 
• Modelled Residue Count: 1,511 
• Deposited Residue Count: 1,576 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], H [auth B], L [auth C], M [auth C], O [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], N [auth C], P [auth D], Q [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: 2.00 Å
• R-Value Free: 0.244 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.144	α = 90
b = 165.408	β = 90
c = 165.666	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-11 
Deposition Author(s): Eswaramoorthy, S., Raparia, E., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2023-11-22
  Changes: Data collection