1PF5 | pdb_00001pf5

Structural Genomics, Protein YJGH

• PDB DOI: https://doi.org/10.2210/pdb1PF5/pdb

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


• Deposited: 2003-05-23 Released: 2003-12-09 
• Deposition Author(s): Zhang, R., Joachimiak, A., Edwards, A., Savchenko, A., Xu, L., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.218 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

The 2.5A crystal structure of protein YJGH from E. Coli

Zhang, R., Joachimiak, A., Edwards, A., Savchenko, A., Xu, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 14.8 kDa 
• Atom Count: 1,084 
• Modeled Residue Count: 130 
• Deposited Residue Count: 131 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein yjgH	A	131	Escherichia coli	Mutation(s): 0  Gene Names: YJGH
UniProt
Find proteins for P39332 (Escherichia coli (strain K12)) Explore P39332  Go to UniProtKB:  P39332

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	B [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.218 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.737	α = 90
b = 127.737	β = 90
c = 127.737	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
d*TREK	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-12-09 
Deposition Author(s): Zhang, R., Joachimiak, A., Edwards, A., Savchenko, A., Xu, L., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2003-12-09
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations