3G3Z

The structure of NMB1585, a MarR family regulator from Neisseria meningitidis

• PDB DOI: https://doi.org/10.2210/pdb3G3Z/pdb

• Classification: TRANSCRIPTION
• Organism(s): Neisseria meningitidis serogroup B
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-03 Released: 2009-04-14 
• Deposition Author(s): Nichols, C.E., Sainsbury, S., Ren, J., Walter, T.S., Verma, A., Stammers, D.K., Saunders, N.J., Owens, R.J., Oxford Protein Production Facility (OPPF)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.266 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

The structure of NMB1585, a MarR-family regulator from Neisseria meningitidis

Nichols, C.E., Sainsbury, S., Ren, J., Walter, T.S., Verma, A., Stammers, D.K., Saunders, N.J., Owens, R.J.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 204-209

• PubMed: 19255465 
• DOI: https://doi.org/10.1107/S174430910900414X
• Primary Citation of Related Structures:  
  3G3Z


• PubMed Abstract: 
  

  The structure of the MarR-family transcription factor NMB1585 from Neisseria meningitidis has been solved using data extending to a resolution of 2.1 A. Overall, the dimeric structure resembles those of other MarR proteins, with each subunit comprising a winged helix-turn-helix (wHtH) domain connected to an alpha-helical dimerization domain. The spacing of the recognition helices of the wHtH domain indicates that NMB1585 is pre-configured for DNA binding, with a putative inducer pocket that is largely occluded by the side chains of two aromatic residues (Tyr29 and Trp53). NMB1585 was shown to bind to its own promoter region in a gel-shift assay, indicating that the protein acts as an auto-repressor.

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Organizational Affiliation: 

Wellcome Trust Centre for Human Genetics, University of Oxford, 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: 32.86 kDa 
• Atom Count: 2,363 
• Modelled Residue Count: 284 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, MarR family	A, B	145	Neisseria meningitidis serogroup B	Mutation(s): 0  Gene Names: NMB1585
UniProt
Find proteins for Q9JYH5 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q9JYH5  Go to UniProtKB:  Q9JYH5

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: 2.10 Å
• R-Value Free:  0.266 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.001	α = 90
b = 64.367	β = 91.12
c = 61.066	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-14 
Deposition Author(s): Nichols, C.E., Sainsbury, S., Ren, J., Walter, T.S., Verma, A., Stammers, D.K., Saunders, N.J., Owens, R.J., Oxford Protein Production Facility (OPPF)

Revision History  

• Version 1.0: 2009-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary