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 3GO5 | pdb_00003go5

Crystal structure of a multidomain protein with nucleic acid binding domains (sp_0946) from streptococcus pneumoniae tigr4 at 1.40 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.175 (Depositor), 0.179 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.155 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3GO5

This is version 1.5 of the entry. See complete history. 

Literature

Structure of a virulence regulatory factor CvfB reveals a novel winged helix RNA binding module.

Matsumoto, Y., Xu, Q., Miyazaki, S., Kaito, C., Farr, C.L., Axelrod, H.L., Chiu, H.J., Klock, H.E., Knuth, M.W., Miller, M.D., Elsliger, M.A., Deacon, A.M., Godzik, A., Lesley, S.A., Sekimizu, K., Wilson, I.A.

(2010) Structure 18: 537-547

  • DOI: https://doi.org/10.1016/j.str.2010.02.007
  • Primary Citation Related Structures: 
    3GO5

  • PubMed Abstract: 

    CvfB is a conserved regulatory protein important for the virulence of Staphylococcus aureus. We show here that CvfB binds RNA. The crystal structure of the CvfB ortholog from Streptococcus pneumoniae at 1.4 A resolution reveals a unique RNA binding protein that is formed from a concatenation of well-known structural modules that bind nucleic acids: three consecutive S1 RNA binding domains and a winged helix (WH) domain. The third S1 and the WH domains are required for cooperative RNA binding and form a continuous surface that likely contributes to the RNA interaction. The WH domain is critical to CvfB function and contains a unique sequence motif. Thus CvfB represents a novel assembly of modules for binding RNA.


  • Organizational Affiliation: 
    • Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan.

Macromolecule Content 

  • Total Structure Weight: 33.55 kDa 
  • Atom Count: 3,255 
  • Modeled Residue Count: 285 
  • Deposited Residue Count: 285 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Multidomain protein with S1 RNA-binding domains285Streptococcus pneumoniae TIGR4Mutation(s): 0 
Gene Names: NP_345429.1, SP_0946
UniProt
Find proteins for A0A0H2UPM3 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore A0A0H2UPM3 
Go to UniProtKB:  A0A0H2UPM3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2UPM3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.175 (Depositor), 0.179 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.155 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.56α = 90
b = 62.56β = 90
c = 160.2γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-02-01
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-11-27
    Changes: Data collection, Structure summary