6J1K | pdb_00006j1k

Crystal structure of ribose-5-phosphate isomerase A from Ochrobactrum sp. CSL1

PDB DOI: https://doi.org/10.2210/pdb6J1K/pdb

Classification: ISOMERASE
Organism(s): Ochrobactrum sp.
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-12-28 Released: 2019-04-17
Deposition Author(s): Xu, X.Q., Mo, X.B., Ju, X., Shen, M., Li, L.Z., Yuan, A.Y.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free:
0.287 (Depositor), 0.292 (DCC)
R-Value Work:
0.236 (Depositor), 0.246 (DCC)
R-Value Observed:
0.238 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6J1K

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

Literature

Crystal structure of ribose-5-phosphate isomerase A from Ochrobactrum sp. CSL1

Xu, X.Q., Mo, X.B., Ju, X., Shen, M., Li, L.Z., Yuan, A.Y.

To be published.

Macromolecule Content

Total Structure Weight: 48.48 kDa
Atom Count: 3,351
Modeled Residue Count: 456
Deposited Residue Count: 464
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose-5-phosphate isomerase A	A, B	232	Ochrobactrum sp.	Mutation(s): 0 EC: 5.3.1.6
UniProt
Find proteins for A6X0Q4 (Brucella anthropi (strain ATCC 49188 / DSM 6882 / CCUG 24695 / JCM 21032 / LMG 3331 / NBRC 15819 / NCTC 12168 / Alc 37)) Explore A6X0Q4 Go to UniProtKB: A6X0Q4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6X0Q4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free: 0.287 (Depositor), 0.292 (DCC)
R-Value Work: 0.236 (Depositor), 0.246 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.817	α = 90
b = 169.262	β = 90
c = 41.268	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-04-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	21376156
National Natural Science Foundation of China	China	21676173

Revision History (Full details and data files)

Version 1.0: 2019-04-17
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.