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)

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Experimental Data Snapshot

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

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 
• DOI: https://doi.org/10.1002/prot.20337
• Primary Citation of Related Structures:  
  1X6I, 1X6J

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 10.85 kDa 
• Atom Count: 774 
• Modelled Residue Count: 88 
• Deposited Residue Count: 91 
• Unique protein chains: 1

Macromolecules

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

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

Entry History 

Deposition Data

• Released Date: 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)

Revision History  

• 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