2IIU | pdb_00002iiu

Crystal structure of a putative PhoU-like phosphate regulatory protein (NP_719307.1) from Shewanella oneidensis MR-1 at 2.28 A resolution.

• PDB DOI: https://doi.org/10.2210/pdb2IIU/pdb

• Classification: Structural Genomics/Unknown function
• Organism(s): Shewanella oneidensis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-09-28 Released: 2006-10-17 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.247 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Crystal structure of conserved hypothetical protein (NP_719307.1) from Shewanella Oneidensis MR-1 at 2.28 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 18-mer - A18 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.9 kDa 
• Atom Count: 5,045 
• Modeled Residue Count: 631 
• Deposited Residue Count: 681 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B, C	227	Shewanella oneidensis	Mutation(s): 6  Gene Names: NP_719307.1
UniProt
Find proteins for Q8EAX1 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8EAX1  Go to UniProtKB:  Q8EAX1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 2.28 Å
• R-Value Free:  0.247 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32IIU

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.88	α = 90
b = 99.88	β = 90
c = 397.27	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-17 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-10-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, 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: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary