4RLG

The clear crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.901 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The clear crystal structure of 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyridoxal-dependent decarboxylase
A, B, D, C
486Sphaerobacter thermophilus (strain DSM 20745 / S 6022)Mutation(s): 0 
Find proteins for D1C7D8 (Sphaerobacter thermophilus (strain DSM 20745 / S 6022))
Go to UniProtKB:  D1C7D8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ABU
Query on ABU

Download SDF File 
Download CCD File 
D
GAMMA-AMINO-BUTANOIC ACID
GAMMA(AMINO)-BUTYRIC ACID
C4 H9 N O2
BTCSSZJGUNDROE-UHFFFAOYSA-N
 Ligand Interaction
PMP
Query on PMP

Download SDF File 
Download CCD File 
A, B, C, D
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
PYRIDOXAMINE-5'-PHOSPHATE
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
LLP
Query on LLP
A, B, C, D
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.901 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.320α = 90.00
b = 124.981β = 99.49
c = 132.760γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXrefinement
HKL-3000data scaling
HKL-3000data collection
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-29
    Type: Initial release