4KTB

The crystal structure of posible asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases from Jonesia denitrificans DSM 20603


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.936 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The crystal structure of posible asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases from Jonesia denitrificans DSM 20603

Tan, K.Kim, Y.Wu, R.Clancy, S.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein
A, B, C, D
194Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / CIP 55134)Mutation(s): 0 
Find proteins for C7R2I1 (Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / CIP 55134))
Go to UniProtKB:  C7R2I1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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: 1.936 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.489α = 90.00
b = 69.809β = 90.04
c = 94.313γ = 90.00
Software Package:
Software NamePurpose
SHELXDphasing
DMphasing
DMmodel building
SBC-Collectdata collection
WARPmodel building
HKL-3000data reduction
HKL-3000phasing
ARPmodel building
PHENIXrefinement
MLPHAREphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-05
    Type: Initial release