1QYA

CRYSTAL STRUCTURE OF E. COLI PROTEIN YDDE

PDB DOI: https://doi.org/10.2210/pdb1QYA/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-09-10 Released: 2004-06-08
Deposition Author(s): Grassick, A., Sulzenbacher, G., Roig-Zamboni, V., Campanacci, V., Cambillau, C., Bourne, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.228
R-Value Work: 0.186
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of E. coli yddE protein reveals a striking homology with diaminopimelate epimerase

Grassick, A., Sulzenbacher, G., Roig-Zamboni, V., Campanacci, V., Cambillau, C., Bourne, Y.

(2004) Proteins 55: 764-767

PubMed: 15103639 Search on PubMed
DOI: https://doi.org/10.1002/prot.20025
Primary Citation of Related Structures:
1QY9, 1QYA

Macromolecule Content

Total Structure Weight: 66.81 kDa
Atom Count: 4,920
Modelled Residue Count: 600
Deposited Residue Count: 614
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOTHETICAL PROTEIN yddE	A, B	307	Escherichia coli	Mutation(s): 0 Gene Names: yddE EC: 5.1
UniProt
Find proteins for P37757 (Escherichia coli (strain K12)) Explore P37757 Go to UniProtKB: P37757
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P37757
Protein Feature View Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.228
R-Value Work: 0.186
R-Value Observed: 0.188
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.159	α = 90
b = 79.631	β = 115.26
c = 77.022	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-06-08

Deposition Author(s):

Sulzenbacher, G.

Roig-Zamboni, V.

Revision History (Full details and data files)

Version 1.0: 2004-06-08
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance

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.