3U4F

Crystal structure of a mandelate racemase (muconate lactonizing enzyme family protein) from Roseovarius nubinhibens

• PDB DOI: https://doi.org/10.2210/pdb3U4F/pdb

• Classification: ISOMERASE
• Organism(s): Roseovarius nubinhibens ISM
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-10-07 Released: 2011-10-19 
• Deposition Author(s): Eswaramoorthy, S., Kumaran, D., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.207 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

Crystal structure of a mandelate racemase (muconate lactonizing enzyme family protein) from Roseovarius nubinhibens

Eswaramoorthy, S., Kumaran, D., Almo, S.C., Swaminathan, S.

To be published.

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 (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 177.02 kDa 
• Atom Count: 12,194 
• Modelled Residue Count: 1,482 
• Deposited Residue Count: 1,552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme family protein	A, B, C, D	388	Roseovarius nubinhibens ISM	Mutation(s): 0  Gene Names: ISM_12500
UniProt
Find proteins for A3SMJ4 (Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM)) Explore A3SMJ4  Go to UniProtKB:  A3SMJ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GAI	F [auth A], I [auth B], L [auth C], O [auth D]	GUANIDINE C H5 N3 ZRALSGWEFCBTJO-UHFFFAOYSA-N
MG	E [auth A], G [auth A], H [auth B], J [auth B], K [auth C], M [auth C], N [auth D], 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: 1.90 Å
• R-Value Free: 0.207 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.871	α = 90
b = 125.871	β = 90
c = 98.017	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-19 
Deposition Author(s): Eswaramoorthy, S., Kumaran, D., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2011-10-19
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection