1XRU

Crystal Structure of 5-keto-4-deoxyuronate Isomerase from Eschericia coli

PDB DOI: https://doi.org/10.2210/pdb1XRU/pdb

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

Deposited: 2004-10-15 Released: 2005-04-05
Deposition Author(s): Crowther, R.L., Georgiadis, M.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.191
R-Value Work: 0.164
R-Value Observed: 0.165

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of 5-keto-4-deoxyuronate isomerase from Escherichia coli

Crowther, R.L., Georgiadis, M.M.

(2005) Proteins 61: 680-684

PubMed: 16152643 Search on PubMed
DOI: https://doi.org/10.1002/prot.20598
Primary Citation of Related Structures:
1XRU

Organizational Affiliation

The Waksman Institute, Rutgers University, Piscataway, New Jersey, USA.

Macromolecule Content

Total Structure Weight: 64.36 kDa
Atom Count: 4,890
Modelled Residue Count: 562
Deposited Residue Count: 564
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	A, B	282	Escherichia coli	Mutation(s): 11 Gene Names: kduI EC: 5.3.1.17
UniProt
Find proteins for Q46938 (Escherichia coli (strain K12)) Explore Q46938 Go to UniProtKB: Q46938
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q46938
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.191
R-Value Work: 0.164
R-Value Observed: 0.165
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.972	α = 90
b = 102.972	β = 90
c = 176.862	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-04-05

Deposition Author(s):

Crowther, R.L.

Georgiadis, M.M.

Revision History (Full details and data files)

Version 1.0: 2005-04-05
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance

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1XRU

Crystal Structure of 5-keto-4-deoxyuronate Isomerase from Eschericia coli

The crystal structure of 5-keto-4-deoxyuronate isomerase from Escherichia coli

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)