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 OPM PDBTM MemProtMD

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.17 Å
R-Value Free:
0.269 (Depositor), 0.279 (DCC)
R-Value Work:
0.210 (Depositor), 0.223 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal Structures of OccK Subfamily Proteins

Eren, E., van den Berg, B.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I4U9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.17 Å
R-Value Free: 0.269 (Depositor), 0.279 (DCC)
R-Value Work: 0.210 (Depositor), 0.223 (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

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Entry History

Deposition Data

Released Date: 2013-07-24

Deposition Author(s):

van den Berg, B.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.