2GPI | pdb_00002gpi

Crystal structure of a protein of unknown function from duf1488 family (shew_3726) from shewanella loihica pv-4 at 1.60 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2GPI/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Shewanella loihica PV-4
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-04-17 Released: 2006-06-13 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.172 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Literature

Crystal structure of conserved hypothetical protein (ZP_00837230.1) from Shewanella sp. PV-4 at 1.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.67 kDa 
• Atom Count: 861 
• Modeled Residue Count: 91 
• Deposited Residue Count: 91 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
conserved hypothetical protein	A	91	Shewanella loihica PV-4	Mutation(s): 2  Gene Names: ZP_00837230.1
UniProt
Find proteins for A3QJE4 (Shewanella loihica (strain ATCC BAA-1088 / PV-4)) Explore A3QJE4  Go to UniProtKB:  A3QJE4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [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: 1.60 Å
• R-Value Free:  0.172 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32GPI

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.03	α = 90
b = 83.25	β = 90
c = 58.28	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-13 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-06-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary