2O5H | pdb_00002o5h

Uncharacterized Protein Conserved in Bacteria, COG3792 from Neisseria meningitidis

PDB DOI: https://doi.org/10.2210/pdb2O5H/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Neisseria meningitidis MC58
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-12-06 Released: 2007-01-09
Deposition Author(s): Kim, Y., Li, H., Gu, M., Bargassa, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.249 (Depositor), 0.254 (DCC)
R-Value Work:
0.201 (Depositor)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2O5H

This is version 1.5 of the entry. See complete history.

Literature

Uncharacterized Protein Conserved in Bacteria, COG3792 from Neisseria meningitidis

Kim, Y., Li, H., Gu, M., Bargassa, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 32.59 kDa
Atom Count: 2,445
Modeled Residue Count: 246
Deposited Residue Count: 272
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B	136	Neisseria meningitidis MC58	Mutation(s): 2 Gene Names: NMB0513
UniProt
Find proteins for Q9K0R7 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q9K0R7 Go to UniProtKB: Q9K0R7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9K0R7
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: 1.90 Å
R-Value Free: 0.249 (Depositor), 0.254 (DCC)
R-Value Work: 0.201 (Depositor)
R-Value Observed: 0.206 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.822	α = 90
b = 67.153	β = 90
c = 93.777	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXCD	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
SOLVE	phasing
RESOLVE	phasing
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-01-09

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-01-09
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.5: 2024-10-16
Changes: 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.