4E5T | pdb_00004e5t

Crystal structure of a putative Mandelate racemase/Muconate lactonizing enzyme (Target PSI-200750) from Labrenzia alexandrii DFL-11

PDB DOI: https://doi.org/10.2210/pdb4E5T/pdb

Classification: ISOMERASE
Organism(s): Roseibium alexandrii DFL-11
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-03-14 Released: 2012-03-28
Deposition Author(s): Kumar, P.R., Bonanno, J., Chowdhury, S., Foti, R., Gizzi, A., Glen, S., 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: 2.90 Å
R-Value Free:
0.242 (Depositor), 0.237 (DCC)
R-Value Work:
0.164 (Depositor), 0.160 (DCC)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4E5T

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

Literature

Crystal structure of a putative MR/ML enzyme from Labrenzia alexandrii DFL-11

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

To be published.

Macromolecule Content

Total Structure Weight: 354.76 kDa
Atom Count: 23,681
Modeled Residue Count: 3,051
Deposited Residue Count: 3,232
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	404	Roseibium alexandrii DFL-11	Mutation(s): 0 Gene Names: SADFL11_187

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain O [auth G] SDF format, chain N [auth F] SDF format, chain M [auth E] SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain P [auth H] MOL2 format, chain O [auth G] MOL2 format, chain N [auth F] MOL2 format, chain M [auth E] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain P [auth H] mmCIF format, chain O [auth G] mmCIF format, chain N [auth F] mmCIF format, chain M [auth E] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.242 (Depositor), 0.237 (DCC)
R-Value Work: 0.164 (Depositor), 0.160 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.9	α = 90
b = 156.88	β = 90
c = 218.24	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-03-28

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2012-03-28
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.