1MW5

Structure of HI1480 from Haemophilus influenzae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Novel structure and nucleotide binding properties of HI1480 from Haemophilus influenzae: a protein with no known sequence homologues

Lim, K.Sarikaya, E.Galkin, A.Krajewski, W.Pullalarevu, S.Shin, J.H.Kelman, Z.Howard, A.Herzberg, O.

(2004) PROTEINS: STRUCT.,FUNCT.,GENET. 56: 564-571

  • DOI: 10.1002/prot.20148

  • PubMed Abstract: 
  • The crystal structure of the Haemophilus influenzae protein HI1480 was determined at 2.1-A resolution. The amino acid sequence of HI1480 is unique, having no homology with other known protein sequences. The protein adopts a novel alpha+beta fold, and ...

    The crystal structure of the Haemophilus influenzae protein HI1480 was determined at 2.1-A resolution. The amino acid sequence of HI1480 is unique, having no homology with other known protein sequences. The protein adopts a novel alpha+beta fold, and associates into a dimer of tightly associated dimers. The tight dimers are formed by intermolecular interactions that are mediated by an antiparallel beta-barrel involving both monomers. Helical regions of two dimers mediate the tetramer formation. The helical region contains a four-helix bundle that has been seen only in the anticodon binding domains of class I tRNA synthetases. A cluster of four residues, Tyr18, Arg134, Glu26, and Lys12 is located in a depression formed at the four-helix bundle/ beta-barrel interface. The arrangement is suggestive of an active center, possibly a catalytic site. The HI1480 gene is located within the Mu-like prophage region of H. influenzae, has no homology to bacteriophage genes, and is flanked by transposases. Hence, this is an example of horizontal transfer from an unknown organism. Gel mobility shift assays revealed that HI1480 binds DNA and RNA molecules. Double-stranded DNA is favored over single-stranded DNA, and longer DNA molecules are bound better than shorter ones.


    Organizational Affiliation

    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYPOTHETICAL PROTEIN HI1480
A, B
187Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)N/A
Find proteins for P44209 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Go to UniProtKB:  P44209
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.196 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 79.289α = 90.00
b = 79.289β = 90.00
c = 143.842γ = 120.00
Software Package:
Software NamePurpose
DMphasing
SHELXDphasing
SCALEPACKdata scaling
CNSrefinement
ARP/wARPmodel building
DMmodel building
DENZOdata reduction
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description