3LNL

Crystal structure of Staphylococcus aureus protein SA1388


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a Conserved Hypothetical Protein Sa1388 from S. aureus Reveals a Capped Hexameric Toroid with Two Pii Domain Lids and a Dinuclear Metal Center.

Singh Saikatendu, K.Zhang, X.Kinch, L.Leybourne, M.Grishin, N.V.Zhang, H.

(2006) BMC Struct Biol 6: 27

  • DOI: 10.1186/1472-6807-6-27
  • Primary Citation of Related Structures:  
    3LNL, 2NYD

  • PubMed Abstract: 
  • The protein encoded by the SA1388 gene from Staphylococcus aureus was chosen for structure determination to elucidate its domain organization and confirm our earlier remote homology based prediction that it housed a nitrogen regulatory PII protein-like domain ...

    The protein encoded by the SA1388 gene from Staphylococcus aureus was chosen for structure determination to elucidate its domain organization and confirm our earlier remote homology based prediction that it housed a nitrogen regulatory PII protein-like domain. SA1388 was predicted to contain a central PII-like domain and two flanking regions, which together belong to the NIF3-like protein family. Proteins like SA1388 remain a poorly studied group and their structural characterization could guide future investigations aimed at understanding their function.


    Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas TX 75390-8816, USA. skumar@scripps.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UPF0135 protein SA1388A, B370Staphylococcus aureus subsp. aureus N315Mutation(s): 2 
Gene Names: SA1388
Find proteins for P67273 (Staphylococcus aureus (strain N315))
Explore P67273 
Go to UniProtKB:  P67273
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B3P
Query on B3P

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], F [auth B], G [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.547α = 90
b = 132.547β = 90
c = 125.67γ = 120
Software Package:
Software NamePurpose
SBC-Collectdata collection
SOLVEphasing
HKL-3000phasing
REFMACrefinement
Cootmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description