1KNJ

Co-Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate Synthase (ispF) from E. coli Involved in Mevalonate-Independent Isoprenoid Biosynthesis, Complexed with CMP/MECDP/Mn2+

Structural Biology Knowledgebase: 1KNJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.241

Literature

Macromolecules
Sequence Display for 1KNJ

Classification: METAL BINDING PROTEIN

Total Structure Weight: 17764.49

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
Mutation: M1M, M105M, M112M, M124M
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)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-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: 2.8 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.241
  • Space Group: I 21 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 144.25 α = 90.00
b = 144.25 β = 90.00
c = 144.25 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-12-18
  • Released Date: 2002-06-18
  • Deposition author(s): Richard, S.B., Ferrer, J.L., Bowman, M.E., Lillo, A.M., Tetzlaff, C.N., Cane, D.E., Noel, J.P.

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