4DJD

Crystal structure of folate-free corrinoid iron-sulfur protein (CFeSP) in complex with its methyltransferase (MeTr)

Structural Biology Knowledgebase: 4DJD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.187

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DJD

Classification: TRANSFERASE / VITAMIN-BINDING PROTEIN

Total Structure Weight: 228271.58

Macromolecule Entities
Molecule Chains Length Organism Details
5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase A, B 262 Moorella thermoacetica EC#: 2.1.1.258 IUBMB
Gene Name(s): acsE
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Corrinoid/iron-sulfur protein large subunit C, E 446 Moorella thermoacetica Gene Name(s): acsC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Corrinoid/iron-sulfur protein small subunit D, F 323 Moorella thermoacetica Gene Name(s): acsD
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
B12
Query on B12

C, E COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

C, E IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

D, E, F GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.187
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 125.61 α = 90.00
b = 242.84 β = 90.00
c = 79.67 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-01
  • Released Date: 2012-03-14
  • Deposition author(s): Kung, Y., Doukov, T.I., Blasiak, L.C., Drennan, C.L.

Revision History

  • 2012-10-24
    Type: Non-polymer description | Details: update B12 formula
  • 2012-04-25
    Type: Citation | Details: Citation update
  • 2012-03-28
    Type: Citation | Details: Citation update