3M1T

Crystal structure of Putative phosphohydrolase (YP_929327.1) from Shewanella amazonensis SB2B at 1.62 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3M1T/pdb

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


• Deposited: 2010-03-05 Released: 2010-03-31 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.201 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

Literature

Crystal structure of Putative phosphohydrolase (YP_929327.1) from Shewanella amazonensis SB2B at 1.62 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

Macromolecule Content

• Total Structure Weight: 29.96 kDa 
• Atom Count: 2,469 
• Modelled Residue Count: 269 
• Deposited Residue Count: 275 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phosphohydrolase	A	275	Shewanella amazonensis SB2B	Mutation(s): 0  Gene Names: Sama_3455
UniProt
Find proteins for A1SBA1 (Shewanella amazonensis (strain ATCC BAA-1098 / SB2B)) Explore A1SBA1  Go to UniProtKB:  A1SBA1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.62 Å
• R-Value Free: 0.201 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: P 3₁ 2 1
• Diffraction Data: https://doi.org/10.18430/M33M1T

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.729	α = 90
b = 69.729	β = 90
c = 124.569	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-31 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations