1X6I | pdb_00001x6i

Crystal structure of ygfY from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb1X6I/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: 1.20 Å
R-Value Free:
0.211 (Depositor), 0.227 (DCC)
R-Value Work:
0.171 (Depositor), 0.188 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 1X6I

This is version 1.5 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 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: 21.69 kDa
Atom Count: 1,802
Modeled Residue Count: 176
Deposited Residue Count: 182
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ygfY	A, B	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P64559
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.211 (Depositor), 0.227 (DCC)
R-Value Work: 0.171 (Depositor), 0.188 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.5	α = 90
b = 87.1	β = 90
c = 40.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
MLPHARE	phasing
RESOLVE	model building
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
CrystalClear	data scaling
RESOLVE	phasing

Structure Validation

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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: 2019-07-24
Changes: Data collection, Refinement description
Version 1.4: 2019-08-14
Changes: Data collection
Version 1.5: 2024-02-14
Changes: Data collection, Database references

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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.