2OPK | pdb_00002opk

CRYSTAL STRUCTURE OF A PUTATIVE MANNOSE-6-PHOSPHATE ISOMERASE (REUT_A1446) FROM RALSTONIA EUTROPHA JMP134 AT 2.10 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb2OPK/pdb

Classification: ISOMERASE
Organism(s): Cupriavidus pinatubonensis JMP134
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-01-29 Released: 2007-02-13
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.207 (Depositor), 0.216 (DCC)
R-Value Work:
0.166 (Depositor), 0.177 (DCC)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of hypothetical protein (YP_295660.1) from Ralstonia eutropha JMP134 at 2.10 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 50.13 kDa
Atom Count: 3,918
Modeled Residue Count: 440
Deposited Residue Count: 448
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B, C, D	112	Cupriavidus pinatubonensis JMP134	Mutation(s): 3 Gene Names: YP_295660.1, Reut_A1446
UniProt
Find proteins for Q471W7 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q471W7 Go to UniProtKB: Q471W7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q471W7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], I [auth B], L [auth C], N [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C] mmCIF format, chain J [auth C]	J [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth C] Interactions & Density Focus chain J [auth C]
UNL Query on UNL Download:Ideal Coordinates CCD File	E [auth A], H [auth B], K [auth C], M [auth D]	Unknown ligand VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [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: 2.10 Å
R-Value Free: 0.207 (Depositor), 0.216 (DCC)
R-Value Work: 0.166 (Depositor), 0.177 (DCC)
R-Value Observed: 0.168 (Depositor)

Diffraction Data:

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.58	α = 90
b = 75.58	β = 90
c = 198.87	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SOLVE	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-02-13

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-02-13
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2017-10-25
Changes: Author supporting evidence
Version 1.5: 2023-01-25
Changes: Database references, Derived calculations
Version 1.6: 2024-10-30
Changes: Data collection, Refinement description, Structure summary