1M1Y

Chemical Crosslink of Nitrogenase MoFe Protein and Fe Protein

Structural Biology Knowledgebase: 1M1Y SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.329
  • R-Value Work: 0.279

Literature

Macromolecules
Sequence Display for 1M1Y

Classification: OXIDOREDUCTASE

Total Structure Weight: 718066.50

Macromolecule Entities
Molecule Chains Length Organism Details
Nitrogenase molybdenum-iron protein alpha chain A, C, I, K 491 Azotobacter vinelandii EC#: 1.18.6.1 IUBMB
Gene Name(s): nifD
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Nitrogenase molybdenum-iron protein beta chain B, D, J, L 522 Azotobacter vinelandii EC#: 1.18.6.1 IUBMB
Gene Name(s): nifK
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
nitrogenase IRON protein 1 E, F, G..., H, M, N, O, PE, F, G, H, M, N, O, P 289 Azotobacter vinelandii EC#: 1.18.6.1 IUBMB
Gene Name(s): nifH1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CFM
Query on CFM

A, C, I, K FE-MO-S CLUSTER
Fe7 Mo S9
UZRXIPMKRKMLQF-VGXFRCDIAP
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CLF
Query on CLF

A, D, J, K FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-DHHOTQGYAO
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

E, G, N, P IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HCA
Query on HCA

A, C, I, K 3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

B, D, J, L CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.329
  • R-Value Work: 0.279
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 113.27 α = 90.00
b = 214.94 β = 90.00
c = 320.47 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-06-20
  • Released Date: 2003-02-11
  • Deposition author(s): Schmid, B., Einsle, O., Chiu, H.J., Willing, A., Yoshida, M., Howard, J.B., Rees, D.C.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4