4JHM | pdb_00004jhm

Crystal structure of a putative mandelate racemase/muconate lactonizing enzyme from Pseudovibrio sp.

• PDB DOI: https://doi.org/10.2210/pdb4JHM/pdb

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


• Deposited: 2013-03-05 Released: 2013-05-01 
• Deposition Author(s): Hegde, R.P., Toro, R., Burley, S.K., Almo, S.C., Ramagopal, U.A., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a putative mandelate racemase/muconate lactonizing enzyme from Pseudovibrio sp.

Hegde, R.P., Toro, R., Burley, S.K., Almo, S.C., Ramagopal, U.A., New York Structural Genomics Research Consortium (NYSGRC)

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: 350.77 kDa 
• Atom Count: 23,568 
• Modelled Residue Count: 2,997 
• Deposited Residue Count: 3,072 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase / muconate lactonizing enzyme, C-terminal domain protein	A, B, C, D, E, F, G, H	384	Pseudovibrio sp. JE062	Mutation(s): 0  Gene Names: PJE062_89, PJE062_892

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.793	α = 90
b = 117.313	β = 99.77
c = 143.127	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-01 
Deposition Author(s): Hegde, R.P., Toro, R., Burley, S.K., Almo, S.C., Ramagopal, U.A., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-05-01
  Type: Initial release
  
• Version 1.1: 2013-05-08
  Changes: Other
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2023-12-06
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Structure summary