3GXH | pdb_00003gxh

Crystal structure of Putative phosphatase (DUF442) (YP_001181608.1) from SHEWANELLA PUTREFACIENS CN-32 at 1.40 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3GXH/pdb

• Classification: HYDROLASE
• Organism(s): Shewanella putrefaciens CN-32
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-02 Released: 2009-04-21 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.179 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Literature

Crystal structure of Putative phosphatase (DUF442) (YP_001181608.1) from SHEWANELLA PUTREFACIENS CN-32 at 1.40 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.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.27 kDa 
• Atom Count: 2,943 
• Modeled Residue Count: 307 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phosphatase (DUF442)	A, B	157	Shewanella putrefaciens CN-32	Mutation(s): 0  Gene Names: Sputcn32_0073, YP_001181608.1
UniProt
Find proteins for A4Y1H6 (Shewanella putrefaciens (strain CN-32 / ATCC BAA-453)) Explore A4Y1H6  Go to UniProtKB:  A4Y1H6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth A], K [auth B], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.40 Å
• R-Value Free:  0.179 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33GXH

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.303	α = 90
b = 57.528	β = 90
c = 92.364	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-04-21
  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: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-27
  Changes: Data collection, Refinement description, Structure summary