3U4F | pdb_00003u4f

Crystal structure of a mandelate racemase (muconate lactonizing enzyme family protein) from Roseovarius nubinhibens

PDB DOI: https://doi.org/10.2210/pdb3U4F/pdb

Classification: ISOMERASE
Organism(s): Roseovarius nubinhibens ISM
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-10-07 Released: 2011-10-19
Deposition Author(s): Eswaramoorthy, S., Kumaran, D., 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: 1.90 Å
R-Value Free:
0.207 (Depositor), 0.210 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a mandelate racemase (muconate lactonizing enzyme family protein) from Roseovarius nubinhibens

Eswaramoorthy, S., Kumaran, D., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 177.02 kDa
Atom Count: 12,194
Modeled Residue Count: 1,482
Deposited Residue Count: 1,552
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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	388	Roseovarius nubinhibens ISM	Mutation(s): 0 Gene Names: ISM_12500
UniProt
Find proteins for A3SMJ4 (Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM)) Explore A3SMJ4 Go to UniProtKB: A3SMJ4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3SMJ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GAI Query on GAI Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	F [auth A], I [auth B], L [auth C], O [auth D]	GUANIDINE C H₅ N₃ ZRALSGWEFCBTJO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain M [auth C] SDF format, chain N [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D]	E [auth A] G [auth A] H [auth B] J [auth B] K [auth C] E [auth A], G [auth A], H [auth B], J [auth B], K [auth C], M [auth C], N [auth D], P [auth D], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain P [auth D] Focus chain Q [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.207 (Depositor), 0.210 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.871	α = 90
b = 125.871	β = 90
c = 98.017	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-10-19

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2011-10-19
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 1.3: 2024-11-06
Changes: Structure summary