5D1I | pdb_00005d1i

Structure of Cyclic nucleotide-binding-like protein from Brucella abortus bv. 1 str. 9-941


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.233 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5D1I

This is version 1.2 of the entry. See complete history

Literature

Crystal structure of cyclic nucleotide-binding-like protein from Brucella abortus

He, Z.Gao, Y.Dong, J.Ke, Y.Li, X.Chen, Z.Zhang, X.C.

(2015) Biochem Biophys Res Commun 468: 647-652

  • DOI: https://doi.org/10.1016/j.bbrc.2015.11.005
  • Primary Citation Related Structures: 
    5D1I

  • PubMed Abstract: 

    The cyclic nucleotide-binding (CNB)-like protein (CNB-L) from Brucella abortus shares sequence homology with CNB domain-containing proteins. We determined the crystal structure of CNB-L at 2.0 Å resolution in the absence of its C-terminal helix and nucleotide. The 3D structure of CNB-L is in a two-fold symmetric form. Each protomer shows high structure similarity to that of cGMP-binding domain-containing proteins, and likely mimics their nucleotide-free conformation. A key residue, Glu17, mediates the dimerization and prevents binding of cNMP to the canonical ligand-pocket. The structurally observed dimer of CNB-L is stable in solution, and thus is likely to be biologically relevant.


  • Organizational Affiliation
    • National Laboratory of Macromolecules, National Center of Protein Science- Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.

Macromolecule Content 

  • Total Structure Weight: 28.91 kDa 
  • Atom Count: 1,955 
  • Modeled Residue Count: 233 
  • Deposited Residue Count: 262 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyclic nucleotide-binding protein
A, B
131Brucella abortus bv. 1 str. 9-941Mutation(s): 0 
Gene Names: BruAb1_1980
UniProt
Find proteins for Q57AQ0 (Brucella abortus biovar 1 (strain 9-941))
Explore Q57AQ0 
Go to UniProtKB:  Q57AQ0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57AQ0
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.233 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.096α = 90
b = 82.911β = 90
c = 103.918γ = 90
Software Package:
Software NamePurpose
DENZOdata collection
HKL-2000data scaling
PHASESphasing
RESOLVEmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2016-01-13
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary