2IKB

Crystal Structure of a Protein of Unknown Function NMB1012 from Neisseria meningitidis

PDB DOI: https://doi.org/10.2210/pdb2IKB/pdb

Classification: Structural genomics, unknown function
Organism(s): Neisseria meningitidis MC58
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2006-10-02 Released: 2006-11-21
Deposition Author(s): Zhang, R., Li, H., Bargassa, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.247 (Depositor), 0.259 (DCC)
R-Value Work:
0.195 (Depositor), 0.209 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The 1.7 A crystal structure of a hypothetical protein NMB1012 from Neisseria meningitidis

Zhang, R., Li, H., Bargassa, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 75.7 kDa
Atom Count: 5,624
Modelled Residue Count: 642
Deposited Residue Count: 668
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein NMB1012	A, B, C, D	167	Neisseria meningitidis MC58	Mutation(s): 5
UniProt
Find proteins for Q7DDI9 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q7DDI9 Go to UniProtKB: Q7DDI9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7DDI9
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.247 (Depositor), 0.259 (DCC)
R-Value Work: 0.195 (Depositor), 0.209 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.335	α = 90
b = 52.087	β = 90.68
c = 128.874	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-11-21

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2006-11-21
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Refinement description, Source and taxonomy, Version format compliance
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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.