1TQJ

Crystal structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb1TQJ/pdb

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

Deposited: 2004-06-17 Released: 2004-08-31
Deposition Author(s): Wise, E.L., Akana, J., Gerlt, J.A., Rayment, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.220
R-Value Work: 0.170
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

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

Literature

Structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 A resolution.

Wise, E.L., Akana, J., Gerlt, J.A., Rayment, I.

(2004) Acta Crystallogr D Biol Crystallogr 60: 1687-1690

PubMed: 15333955 Search on PubMed
DOI: https://doi.org/10.1107/S0907444904015896
Primary Citation of Related Structures:
1TQJ

PubMed Abstract:
The crystal structure of D-ribulose 5-phosphate 3-epimerase (RPE) from the cyanobacterium Synechocystis was determined by X-ray crystallography to 1.6 A resolution. The enzyme, which catalyzes the epimerization of D-ribulose 5-phosphate and D-xylulose 5-phosphate, assembles as a hexamer of (beta/alpha)(8)-barrels in the crystallographic asymmetric unit. The active site is highly similar to those of two previously reported RPEs and provides further evidence for essential catalytic roles for several active-site residues.

Organizational Affiliation

Deparment of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.

Macromolecule Content

Total Structure Weight: 149.99 kDa
Atom Count: 11,308
Modelled Residue Count: 1,297
Deposited Residue Count: 1,380
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose-phosphate 3-epimerase	A, B, C, D, E A, B, C, D, E, F	230	Synechocystis sp.	Mutation(s): 0 Gene Names: RPE, SLL0807 EC: 5.1.3.1
UniProt
Find proteins for P74061 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P74061 Go to UniProtKB: P74061
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P74061
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.220
R-Value Work: 0.170
R-Value Observed: 0.173
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.564	α = 90
b = 87.779	β = 114.58
c = 97.821	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
COMO	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-08-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-08-31
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references

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.