2IFX

Crystal structure of a putative 4-methylmuconolactone methylisomerase (YP_295714.1) from Ralstonia eutropha JMP134 at 2.00 A resolution

PDB DOI: https://doi.org/10.2210/pdb2IFX/pdb

Classification: Structural Genomics/Unknown function
Organism(s): Cupriavidus necator
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-09-21 Released: 2006-10-10
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.202
R-Value Work: 0.171
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of hypothetical protein (YP_295714.1) from Ralstonia Eutropha JMP134 at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 26.49 kDa
Atom Count: 1,814
Modelled Residue Count: 203
Deposited Residue Count: 228
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B	114	Cupriavidus necator	Mutation(s): 4 Gene Names: YP_295714.1
UniProt
Find proteins for Q471R3 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q471R3 Go to UniProtKB: Q471R3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q471R3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B]	D [auth A], E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.202
R-Value Work: 0.171
R-Value Observed: 0.173
Space Group: P 4₃
Diffraction Data: https://doi.org/10.18430/M32IFX

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.06	α = 90
b = 46.06	β = 90
c = 124.16	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SOLVE	phasing
RESOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-10-10

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2006-10-10
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.