2R2C | pdb_00002r2c

Crystal structure of a domain of the outer membrane lipoprotein Omp28 from Porphyromonas gingivalis

PDB DOI: https://doi.org/10.2210/pdb2R2C/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Porphyromonas gingivalis W83
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2007-08-24 Released: 2007-09-25
Deposition Author(s): Zhang, R., Hatzos, C., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.201 (Depositor), 0.200 (DCC)
R-Value Work:
0.174 (Depositor), 0.173 (DCC)
R-Value Observed:
0.175 (Depositor)

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

Literature

The crystal structure of a domain of the outer membrane lipoprotein Omp28 from Porphyromonas gingivalis.

Zhang, R., Hatzos, C., Moy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 41.91 kDa
Atom Count: 2,196
Modeled Residue Count: 230
Deposited Residue Count: 366
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
28 kDa outer membrane protein Omp28	A, B	183	Porphyromonas gingivalis W83	Mutation(s): 0 Gene Names: omp28, PG_2173
UniProt
Find proteins for Q9S3Q1 (Porphyromonas gingivalis) Explore Q9S3Q1 Go to UniProtKB: Q9S3Q1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9S3Q1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.201 (Depositor), 0.200 (DCC)
R-Value Work: 0.174 (Depositor), 0.173 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.831	α = 90
b = 110.342	β = 90
c = 90.73	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-09-25

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-09-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.