3T4W | pdb_00003t4w

The crystal structure of mandelate racemase/muconate lactonizing enzyme from Sulfitobacter sp

PDB DOI: https://doi.org/10.2210/pdb3T4W/pdb

Classification: LYASE
Organism(s): Sulfitobacter sp. NAS-14.1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-07-26 Released: 2011-08-17
Deposition Author(s): Zhang, Z., 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.240 (Depositor), 0.230 (DCC)
R-Value Work:
0.184 (Depositor), 0.180 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of mandelate racemase/muconate lactonizing enzyme from Sulfitobacter sp

Zhang, Z., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 187.12 kDa
Atom Count: 12,495
Modeled Residue Count: 1,584
Deposited Residue Count: 1,728
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme family protein	A, B, C, D	432	Sulfitobacter sp. NAS-14.1	Mutation(s): 0 Gene Names: NAS141_08491
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.240 (Depositor), 0.230 (DCC)
R-Value Work: 0.184 (Depositor), 0.180 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.564	α = 90
b = 170.176	β = 90
c = 84.429	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-08-17

Deposition Author(s):

Swaminathan, S.

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2011-08-17
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Refinement description

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.