2QVP

CRYSTAL STRUCTURE OF A PUTATIVE METALLOPEPTIDASE (SAMA_0725) FROM SHEWANELLA AMAZONENSIS SB2B AT 2.00 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2QVP/pdb

• Classification: HYDROLASE
• Organism(s): Shewanella amazonensis SB2B
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-08-08 Released: 2007-08-28 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.213 
• R-Value Work: 0.161 
• R-Value Observed: 0.164 

Literature

Crystal structure of uncharacterized protein (YP_926603.1) from Shewanella amazonensis SB2B at 2.00 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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 93.08 kDa 
• Atom Count: 6,932 
• Modelled Residue Count: 802 
• Deposited Residue Count: 825 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C	275	Shewanella amazonensis SB2B	Mutation(s): 0  Gene Names: YP_926603.1, Sama_0725
UniProt
Find proteins for A1S3H7 (Shewanella amazonensis (strain ATCC BAA-1098 / SB2B)) Explore A1S3H7  Go to UniProtKB:  A1S3H7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], N [auth C], O [auth C], P [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], L [auth B], M [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.213 
• R-Value Work: 0.161 
• R-Value Observed: 0.164 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M32QVP

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.04	α = 90
b = 74.75	β = 95.19
c = 96.12	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-28 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-08-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, 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