1XVI

Crystal Structure of YedP, phosphatase-like domain protein from Escherichia coli K12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of YedP, phosphatase-like domain protein from Escherichia coli K12

Kim, Y.Joachimiak, A.Cymborowski, M.Skarina, T.Savchenko, A.Edwards, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative mannosyl-3-phosphoglycerate phosphataseA, B275Escherichia coli K-12Mutation(s): 0 
Gene Names: yedPb1955JW1938
EC: 3.1.3.70
UniProt
Find proteins for P76329 (Escherichia coli (strain K12))
Explore P76329 
Go to UniProtKB:  P76329
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76329
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
E [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
F [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
G [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.783α = 90
b = 79.975β = 99.56
c = 75.471γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance