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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.297 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

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 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

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 ATCC BAA-335 / MC58)) Explore Q9JZZ4  Go to UniProtKB:  Q9JZZ4

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

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

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary