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 3H9X | pdb_00003h9x

Crystal Structure of the PSPTO_3016 protein from Pseudomonas syringae, Northeast Structural Genomics Consortium Target PsR293


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 
    0.245 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3H9X

This is version 1.4 of the entry. See complete history. 

Literature

Solution NMR and X-ray crystal structures of Pseudomonas syringae Pspto_3016 from protein domain family PF04237 (DUF419) adopt a "double wing" DNA binding motif.

Feldmann, E.A., Seetharaman, J., Ramelot, T.A., Lew, S., Zhao, L., Hamilton, K., Ciccosanti, C., Xiao, R., Acton, T.B., Everett, J.K., Tong, L., Montelione, G.T., Kennedy, M.A.

(2012) J Struct Funct Genomics 13: 155-162

  • DOI: https://doi.org/10.1007/s10969-012-9140-8
  • Primary Citation Related Structures: 
    2KFP, 3H9X

  • PubMed Abstract: 

    The protein Pspto_3016 is a 117-residue member of the protein domain family PF04237 (DUF419), which is to date a functionally uncharacterized family of proteins. In this report, we describe the structure of Pspto_3016 from Pseudomonas syringae solved by both solution NMR and X-ray crystallography at 2.5 Å resolution. In both cases, the structure of Pspto_3016 adopts a "double wing" α/β sandwich fold similar to that of protein YjbR from Escherichia coli and to the C-terminal DNA binding domain of the MotA transcription factor (MotCF) from T4 bacteriophage, along with other uncharacterized proteins. Pspto_3016 was selected by the Protein Structure Initiative of the National Institutes of Health and the Northeast Structural Genomics Consortium (NESG ID PsR293).


  • Organizational Affiliation: 
    • Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.

Macromolecule Content 

  • Total Structure Weight: 59.88 kDa 
  • Atom Count: 3,921 
  • Modeled Residue Count: 468 
  • Deposited Residue Count: 500 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
uncharacterized protein PSPTO_3016
A, B, C, D
125Pseudomonas syringae pv. tomatoMutation(s): 0 
Gene Names: PSPTO3016, PSPTO_3016
UniProt
Find proteins for Q880Y4 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000))
Explore Q880Y4 
Go to UniProtKB:  Q880Y4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ880Y4
Sequence Annotations
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Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free:  0.245 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.302α = 87.07
b = 48.546β = 92.4
c = 68.047γ = 93.57
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-10-17
    Changes: Database references
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Data collection, Database references, Structure summary