3L92

Phosphopantetheine adenylyltransferase from Yersinia pestis complexed with coenzyme A.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.192 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted COAClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

X-ray crystal structure of phosphopantetheine adenylyltransferase from Yersinia pestis.

Osipiuk, J.Maltseva, N.Makowska-grzyska, M.Kwon, K.Anderson, W.F.Joachimiak, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphopantetheine adenylyltransferase162Yersinia pestis CO92Mutation(s): 0 
Gene Names: coaDkdtBy0088YPO0053YP_0054
EC: 2.7.7.3
UniProt
Find proteins for Q8ZJN9 (Yersinia pestis)
Explore Q8ZJN9 
Go to UniProtKB:  Q8ZJN9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZJN9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download Ideal Coordinates CCD File 
B [auth A]COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.192 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.82α = 90
b = 114.82β = 90
c = 119.074γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
MOLREPphasing
HKL-3000phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted COAClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2014-10-01
    Changes: Structure summary
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description