4E4U

Crystal structure of a putative Mandelate racemase/Muconate lactonizing enzyme (Target PSI-200780) from Burkholderia SAR-1

PDB DOI: https://doi.org/10.2210/pdb4E4U/pdb

Classification: ISOMERASE
Organism(s): unidentified
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-03-13 Released: 2012-04-18
Deposition Author(s): Kumar, P.R., Bonanno, J., Chowdhury, S., Foti, R., Gizzi, A., Hammonds, J., Hillerich, B., Matikainen, B., Seidel, R., Toro, R., Zencheck, W., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.146 (Depositor), 0.140 (DCC)
R-Value Work:
0.133 (Depositor), 0.130 (DCC)
R-Value Observed:
0.134 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a putative MR/ML enzyme from Burkholderia SAR-1

Kumar, P.R., Bonanno, J., Chowdhury, S., Foti, R., Gizzi, A., Hammonds, J., Hillerich, B., Matikainen, B., Seidel, R., Toro, R., Zencheck, W., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 45.8 kDa
Atom Count: 3,646
Modelled Residue Count: 403
Deposited Residue Count: 412
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandalate racemase/muconate lactonizing enzyme	A	412	unidentified	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DTU Query on DTU Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-ZXZARUISSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.146 (Depositor), 0.140 (DCC)
R-Value Work: 0.133 (Depositor), 0.130 (DCC)
R-Value Observed: 0.134 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.835	α = 90
b = 118.835	β = 90
c = 120.839	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
XDS	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-04-18

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2012-04-18
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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.