1X6J

Crystal structure of ygfY from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb1X6J/pdb

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

Deposited: 2004-08-11 Released: 2005-02-08
Deposition Author(s): Lim, K., Doseeva, V., Sarikaya Demirkan, E., Pullalarevu, S., Krajewski, W., Galkin, A., Howard, A., Herzberg, O., Structure 2 Function Project (S2F)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.242
R-Value Work: 0.188

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the YgfY from Escherichia coli, a protein that may be involved in transcriptional regulation

Lim, K., Doseeva, V., Sarikaya Demirkan, E., Pullalarevu, S., Krajewski, W., Galkin, A., Howard, A., Herzberg, O.

(2005) Proteins 58: 759-763

PubMed: 15593094 Search on PubMed
DOI: https://doi.org/10.1002/prot.20337
Primary Citation of Related Structures:
1X6I, 1X6J

Organizational Affiliation

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.

Macromolecule Content

Total Structure Weight: 10.85 kDa
Atom Count: 774
Modelled Residue Count: 88
Deposited Residue Count: 91
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 ygfY	A	91	Escherichia coli	Mutation(s): 0 Gene Names: ygfY
UniProt
Find proteins for P64559 (Escherichia coli (strain K12)) Explore P64559 Go to UniProtKB: P64559
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P64559
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.242
R-Value Work: 0.188
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.4	α = 90
b = 42.7	β = 90
c = 84.9	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
BEAST	model building
X-PLOR	model building
CNS	refinement
BEAST	phasing
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-02-08

Deposition Author(s):

Sarikaya Demirkan, E.

Pullalarevu, S.

Structure 2 Function Project (S2F)

Revision History (Full details and data files)

Version 1.0: 2005-02-08
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: 2017-10-11
Changes: Refinement description
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 R01GM133198.