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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.253 (Depositor), 0.255 (DCC)
R-Value Work:
0.194 (Depositor), 0.195 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4JHM

This is version 1.5 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 350.77 kDa
Atom Count: 23,568
Modeled Residue Count: 2,997
Deposited Residue Count: 3,072
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase / muconate lactonizing enzyme, C-terminal domain protein	A, B, C, D, E 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 Query on MSE	A, B, C, D, E 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), 0.255 (DCC)
R-Value Work: 0.194 (Depositor), 0.195 (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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-05-01

Deposition Author(s):

Ramagopal, U.A.

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.