3CAM

Crystal structure of the cold shock domain protein from Neisseria meningitidis

PDB DOI: https://doi.org/10.2210/pdb3CAM/pdb

Classification: GENE REGULATION
Organism(s): Neisseria meningitidis MC58
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-02-20 Released: 2008-03-25
Deposition Author(s): Ren, J., Sainsbury, S., Owens, R.J., Oxford Protein Production Facility (OPPF)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.297
R-Value Work: 0.233
R-Value Observed: 0.236

wwPDB Validation 3D Report Full Report

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

Literature

Structure of the cold-shock domain protein from Neisseria meningitidis reveals a strand-exchanged dimer.

Ren, J., Nettleship, J.E., Sainsbury, S., Saunders, N.J., Owens, R.J.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 247-251

PubMed: 18391418 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S1744309108005411
Primary Citation of Related Structures:
3CAM

PubMed Abstract:
The structure of the cold-shock domain protein from Neisseria meningitidis has been solved to 2.6 A resolution and shown to comprise a dimer formed by the exchange of two beta-strands between protein monomers. The overall fold of the monomer closely resembles those of other bacterial cold-shock proteins. The neisserial protein behaved as a monomer in solution and was shown to bind to a hexathymidine oligonucleotide with a stoichiometry of 1:1 and a K(d) of 1.25 microM.

Organizational Affiliation

The Oxford Protein Production Facility, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England.

Macromolecule Content

Total Structure Weight: 14.59 kDa
Atom Count: 1,030
Modelled Residue Count: 134
Deposited Residue Count: 134
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cold-shock domain family protein	A, B	67	Neisseria meningitidis MC58	Mutation(s): 0 Gene Names: NMB0838
UniProt
Find proteins for Q9JZZ4 (Neisseria meningitidis serogroup B (strain MC58)) Explore Q9JZZ4 Go to UniProtKB: Q9JZZ4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9JZZ4
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: 2.60 Å
R-Value Free: 0.297
R-Value Work: 0.233
R-Value Observed: 0.236
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.369	α = 90
b = 59.369	β = 90
c = 89.423	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXCD	phasing
SHELXE	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-03-25

Deposition Author(s):

Oxford Protein Production Facility (OPPF)

Revision History (Full details and data files)

Version 1.0: 2008-03-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.