4RJ0

The crystal structure of Y333N mutant pyridoxal-dependent decarboxylase from Sphaerobacter thermophilus dsm 20745


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation 3D Report Full Report



Literature

The crystal structure of Y333N mutant pyridoxal-dependent decarboxylase from Sphaerobacter thermophilus dsm 20745

Wu, R.Clancy, S.Joachimiak, A.Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyridoxal-dependent decarboxylaseABCD486Sphaerobacter thermophilus DSM 20745Mutation(s): 1 
Gene Names: Sthe_2364
EC: 4.1.1.15
Find proteins for D1C7D8 (Sphaerobacter thermophilus (strain DSM 20745 / S 6022))
Explore D1C7D8 
Go to UniProtKB:  D1C7D8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PMP
Query on PMP

Download CCD File 
D
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A,B,C,DL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.984α = 90
b = 124.198β = 99.56
c = 129.942γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
MLPHAREphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-12
    Type: Initial release