1YWK

Crystal structure of 4-deoxy-1-threo-5-hexosulose-uronate ketol-isomerase from Enterococcus faecalis

PDB DOI: https://doi.org/10.2210/pdb1YWK/pdb

Classification: ISOMERASE
Organism(s): Enterococcus faecalis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-02-18 Released: 2005-03-01
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.265
R-Value Work: 0.241
R-Value Observed: 0.241

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of 4-deoxy-1-threo-5-hexosulose-uronate ketol-isomerase from Enterococcus faecalis V583

Fedorov, A.A., Fedorov, E.V., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 200.22 kDa
Atom Count: 12,252
Modelled Residue Count: 1,523
Deposited Residue Count: 1,734
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1	A, B, C, D, E A, B, C, D, E, F	289	Enterococcus faecalis	Mutation(s): 0 Gene Names: kduI1, kduI-1 EC: 5.3.1.17
UniProt
Find proteins for Q838L9 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q838L9 Go to UniProtKB: Q838L9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q838L9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.265
R-Value Work: 0.241
R-Value Observed: 0.241
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.01	α = 90
b = 107.685	β = 90
c = 191.021	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-03-01

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2005-03-01
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: 2021-02-03
Changes: Database references, Structure summary
Version 1.4: 2024-02-14
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.