6QKB

Crystal structure of the beta-hydroxyaspartate aldolase of Paracoccus denitrificans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.701 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Marine Proteobacteria metabolise glycolate via the beta-hydroxyaspartate cycle

Schada von Borzyskowski, L.Severi, F.Krueger, K.Hermann, L.Gilardet, A.Sippel, F.Claus, P.Cortina, N.S.Glatter, T.Pommerenke, B.Zarzycki, J.Bremer, E.Maier, U.G.Fuchs, B.M.Amann, R.I.Erb, T.J.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-3-hydroxyaspartate aldolase
A, B
387Paracoccus denitrificans (strain Pd 1222)Mutation(s): 0 
EC: 4.1.3.-
Find proteins for A1B8Z1 (Paracoccus denitrificans (strain Pd 1222))
Go to UniProtKB:  A1B8Z1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

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Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.701 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.598α = 90.00
b = 75.247β = 90.00
c = 157.310γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB987
European UnionGermanyFET686330

Revision History 

  • Version 1.0: 2019-08-14
    Type: Initial release