1Q7E

Crystal Structure of YfdW protein from E. coli

Structural Biology Knowledgebase: 1Q7E SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.186
  • R-Value Work: 0.156

Literature

Macromolecules
Sequence Display for 1Q7E

Classification: TRANSFERASE

Total Structure Weight: 48635.41

Macromolecule Entities
Molecule Chains Length Organism Details
Hypothetical protein yfdW A 428 Escherichia coli EC#: 2.8.3.16 IUBMB
Mutation: M27M, M64M, M85M, M176M, M200M, M202M, M343M, M376M, M412M
Gene Name(s): frc yfdW b2374 JW2371
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

A (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
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: 1.6 Å
  • R-Value Free: 0.186
  • R-Value Work: 0.156
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 92.37 α = 90.00
b = 69.61 β = 108.63
c = 73.22 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-08-18
  • Released Date: 2003-09-30
  • Deposition author(s): Gogos, A., Gorman, J., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History

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