4FRT | pdb_00004frt

Crystal Structure of Pseudomonas aeruginosa OccK7 (OpdD)

• PDB DOI: https://doi.org/10.2210/pdb4FRT/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2012-06-26 Released: 2013-07-24 
• Deposition Author(s): Eren, E., van den Berg, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free: 
  0.269 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures of OccK Subfamily Proteins

Eren, E., van den Berg, B.

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 2  

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

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

Macromolecule Content 

• Total Structure Weight: 90.34 kDa 
• Atom Count: 5,916 
• Modeled Residue Count: 744 
• Deposited Residue Count: 800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable porin	A, B	400	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA1025 Membrane Entity: Yes
UniProt
Find proteins for Q9I4U9 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I4U9  Go to UniProtKB:  Q9I4U9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free:  0.269 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.25	α = 90
b = 111.154	β = 123.25
c = 99.933	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Eren, E., van den Berg, B.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2021-07-07
  Changes: Database references, Derived calculations, Other
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Refinement description