3JYF

The crystal structure of a 2,3-cyclic nucleotide 2-phosphodiesterase/3-nucleotidase bifunctional periplasmic precursor protein from Klebsiella pneumoniae subsp. pneumoniae MGH 78578


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The crystal structure of a 2,3-cyclic nucleotide 2-phosphodiesterase/3-nucleotidase bifunctional periplasmic precursor protein from Klebsiella pneumoniae subsp. pneumoniae MGH 78578

Fan, Y.Volkart, L.Cobb, G.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase bifunctional periplasmic protein
A, B
339Klebsiella pneumoniae subsp. pneumoniae MGH 78578Mutation(s): 0 
Gene Names: cpdBKPN78578_45340KPN_04607
Find proteins for A6THC4 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Go to UniProtKB:  A6THC4
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download CCD File 
A, B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
TAM
Query on TAM

Download CCD File 
B
TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.041α = 90
b = 106.041β = 90
c = 182.967γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
ARPmodel building
WARPmodel building
HKL-3000phasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description