2PRX | pdb_00002prx

Crystal structure of Thioesterase superfamily protein (ZP_00837258.1) from Shewanella loihica PV-4 at 1.65 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2PRX/pdb

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


• Deposited: 2007-05-04 Released: 2007-05-29 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.277 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Crystal structure of Thioesterase superfamily protein (ZP_00837258.1) from Shewanella loihica PV-4 at 1.65 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 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 34.91 kDa 
• Atom Count: 1,724 
• Modeled Residue Count: 228 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioesterase superfamily protein	A, B	160	Shewanella loihica PV-4	Mutation(s): 6  Gene Names: ZP_00837258.1, Shew_3755
UniProt
Find proteins for A3QJH3 (Shewanella loihica (strain ATCC BAA-1088 / PV-4)) Explore A3QJH3  Go to UniProtKB:  A3QJH3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.277 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32PRX

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.501	α = 90
b = 38.501	β = 90
c = 172.247	γ = 120

Software Package:

Software Name	Purpose
SHELX	refinement
MolProbity	model building
SOLVE	phasing
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-29 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-05-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2024-11-20
  Changes: Data collection, Structure summary