3IIC | pdb_00003iic

Crystal structure of CheC-like superfamily protein (YP_001095400.1) from Shewanella SP. PV-4 at 2.13 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3IIC/pdb

• Classification: HYDROLASE
• Organism(s): Shewanella loihica PV-4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-31 Released: 2009-08-18 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 
  0.256 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Crystal structure of CheC-like superfamily protein (YP_001095400.1) from Shewanella SP. PV-4 at 2.13 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)

Macromolecule Content 

• Total Structure Weight: 34.54 kDa 
• Atom Count: 2,367 
• Modeled Residue Count: 308 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CheC domain protein	A, B	155	Shewanella loihica PV-4	Mutation(s): 0  Gene Names: Shew_3275, YP_001095400.1
UniProt
Find proteins for A3QI43 (Shewanella loihica (strain ATCC BAA-1088 / PV-4)) Explore A3QI43  Go to UniProtKB:  A3QI43

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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: 2.13 Å
• R-Value Free:  0.256 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33IIC

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.646	α = 90
b = 52.075	β = 90
c = 134.429	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
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-18 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: 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: 2024-10-16
  Changes: Data collection, Refinement description, Structure summary