3FDB

Crystal structure of a putative plp-dependent beta-cystathionase (aecd, dip1736) from corynebacterium diphtheriae at 1.99 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of putative PLP-dependent beta-cystathionase (NP_940074.1) from CORYNEBACTERIUM DIPHTHERIAE at 1.99 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
putative PLP-dependent beta-cystathionase
A
377Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)Mutation(s): 0 
Gene Names: aecD
EC: 3.-.-.-
Find proteins for Q6NFZ9 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Go to UniProtKB:  Q6NFZ9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
LLP
Query on LLP
A
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 69.180α = 90.00
b = 69.180β = 90.00
c = 215.460γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
SHELXphasing
PHENIXrefinement
SHELXDphasing
MolProbitymodel building
PDB_EXTRACTdata extraction
XDSdata reduction
autoSHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description
  • Version 1.3: 2019-07-24
    Type: Data collection, Derived calculations, Refinement description