1G78

X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH PYRIDOXAL 5'-PHOSPHATE AT 2.0 A RESOLUTION

Structural Biology Knowledgebase: 1G78 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.218

Literature

Macromolecules
Sequence Display for 1G78

Classification: OXIDOREDUCTASE

Total Structure Weight: 26960.49

Macromolecule Entities
Molecule Chains Length Organism Details
PYRIDOXINE 5'-PHOSPHATE OXIDASE A 218 Escherichia coli EC#: 1.4.3.5 IUBMB
Mutation: M1M, M53M, M79M, M113M, M127M
Gene Name(s): pdxH b1638 JW1630
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FMN
Query on FMN

A FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE (Synonym)
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PLP
Query on PLP

A PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate (Synonym)
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.218
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 63.40 α = 90.00
b = 63.40 β = 90.00
c = 124.44 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-11-09
  • Released Date: 2000-11-29
  • Deposition author(s): Safo, M.K., Musayev, F.N., di Salvo, M.L., Schirch, V.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values