1WD6 | pdb_00001wd6

crystal structure of JW1657 from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb1WD6/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-05-12 Released: 2004-11-12
Deposition Author(s): Kato-Murayama, M., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.242 (Depositor)
R-Value Work:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1WD6

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

Literature

crystal structure of JW1657 from Escherichia coli

Kato-Murayama, M., Shirouzu, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 27.83 kDa
Atom Count: 1,547
Modeled Residue Count: 193
Deposited Residue Count: 246
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein ydhR	A, B	123	Escherichia coli	Mutation(s): 2 EC: 1
UniProt
Find proteins for P0ACX3 (Escherichia coli (strain K12)) Explore P0ACX3 Go to UniProtKB: P0ACX3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ACX3
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 2.90 Å
R-Value Free: 0.242 (Depositor)
R-Value Work: 0.208 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.803	α = 90
b = 85.803	β = 90
c = 95.923	γ = 120

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-11-12

Deposition Author(s):

Kato-Murayama, M.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2004-11-12
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: 2024-10-23
Changes: Data collection, Database references, Derived calculations, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.