1JY8

2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF)

Structural Biology Knowledgebase: 1JY8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.201

Literature

Macromolecules
Sequence Display for 1JY8

Classification: biosynthetic protein

Total Structure Weight: 17587.33

Macromolecule Entities
Molecule Chains Length Organism Details
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase A 159 Escherichia coli EC#: 4.6.1.12 IUBMB
Gene Name(s): ispF mecS ygbB b2746 JW2716
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
C5P
Query on C5P

A CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CDI
Query on CDI

A 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE
C5 H12 O9 P2
SFRQRNJMIIUYDI-UHNVWZDZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.201
  • Space Group: I 21 3

Unit Cell:

Length (Å) Angle (°)
a = 144.63 α = 90.00
b = 144.63 β = 90.00
c = 144.63 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-09-11
  • Released Date: 2002-01-30
  • Deposition author(s): Steinbacher, S., Kaiser, J., Wungsintaweekul, J., Hecht, S., Eisenreich, W., Gerhardt, S., Bacher, A., Rohdich, F.

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