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), 0.290 (DCC)
R-Value Work:
0.236 (Depositor), 0.250 (DCC)
R-Value Observed:
0.238 (Depositor)

wwPDB Validation 3D Report Full Report

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:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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), 0.290 (DCC)
R-Value Work: 0.236 (Depositor), 0.250 (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

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 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.