3BHN

Crystal structure of a dj-1/pfpi-like protein (shew_2856) from shewanella loihica pv-4 at 1.76 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3BHN/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Shewanella loihica PV-4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-11-28 Released: 2007-12-11 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.190 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 

Literature

Crystal structure of DJ-1 like Protein (YP_001094981.1) from Shewanella loihica PV-4 at 1.76 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.58 kDa 
• Atom Count: 1,893 
• Modelled Residue Count: 214 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ThiJ/PfpI domain protein	A	236	Shewanella loihica PV-4	Mutation(s): 0  Gene Names: YP_001094981.1, Shew_2856
UniProt
Find proteins for A3QGX4 (Shewanella loihica (strain ATCC BAA-1088 / PV-4)) Explore A3QGX4  Go to UniProtKB:  A3QGX4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.190 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 
• Space Group: P 6₁ 2 2
• Diffraction Data: https://doi.org/10.18430/M33BHN

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.32	α = 90
b = 71.32	β = 90
c = 180.63	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-11 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-12-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations