3EXM

Crystal structure of the phosphatase SC4828 with the non-hydrolyzable nucleotide GPCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and mechanism of a new family of prokaryotic nucleoside diphosphatases.

Proudfoot, M.Brown, M.Singer, A.U.Jobin, M.-C.Xu, X.Zheng, H.Chang, C.Edwards, A.M.Joachimiak, A.Savchenko, A.Yakunin, A.F.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatase SC4828 A237Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: SCO5041SCK7.14SCK7.14c
EC: 3.6.1.6
Find proteins for Q9FBN7 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9FBN7 
Go to UniProtKB:  Q9FBN7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GP2
Query on GP2

Download Ideal Coordinates CCD File 
A
PHOSPHOMETHYLPHOSPHONIC ACID GUANOSYL ESTER
C11 H17 N5 O10 P2
OCJWYBKRHNXUME-KQYNXXCUSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.941α = 90
b = 79.706β = 90
c = 82.507γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance