3GBF

Phpd with cadmium complexed with hydroethylphosphonate (HEP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An Unusual Carbon-Carbon Bond Cleavage Reaction in the Biosynthesis of the Herbicide Phosphinothricin

Cicchillio, R.M.Zhang, H.Blodgett, J.A.V.Whitteck, J.T.Li, G.Nair, S.K.van der Donk, W.A.Metcalf, W.W.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PhpD
A
443Streptomyces viridochromogenes (strain DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494)Mutation(s): 0 
Gene Names: hepD (phpD)
EC: 1.13.11.72
Find proteins for Q5IW40 (Streptomyces viridochromogenes (strain DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494))
Go to UniProtKB:  Q5IW40
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2HE
Query on 2HE

Download SDF File 
Download CCD File 
A
(2-hydroxyethyl)phosphonic acid
C2 H7 O4 P
SEHJHHHUIGULEI-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 84.974α = 90.00
b = 94.695β = 90.00
c = 101.595γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
SHARPphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-02-19 
  • Released Date: 2009-06-09 
  • Deposition Author(s): Zhang, H., Nair, S.K.

Revision History 

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance