1NF4

X-Ray Structure of the Desulfovibrio desulfuricans bacterioferritin: the diiron site in different states (reduced structure)

Structural Biology Knowledgebase: 1NF4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.231

Literature

Macromolecules
Sequence Display for 1NF4

Classification: IRON STORAGE / ELECTRON TRANSPORT

Total Structure Weight: 331337.63

Macromolecule Entities
Molecule Chains Length Organism Details
bacterioferritin A, B, C..., D, E, F, G, H, I, J, K, L, M, N, O, PA, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P 179 Desulfovibrio desulfuricans EC#: 1.16.3.1 IUBMB
Gene Name(s): bfr Ddes_1387
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, C, E, G, I, L, M, P 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX
FE-COPROPORPHYRIN III (Synonym)
C36 H36 Fe N4 O8
FEDZMOFKVKOYTI-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.231
  • Space Group: P 21 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 225.68 α = 90.00
b = 225.68 β = 90.00
c = 225.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-12-13
  • Released Date: 2003-04-01
  • Deposition author(s): Macedo, S., Romao, C.V., Mitchell, E., Matias, P.M., Liu, M.Y., Xavier, A.V., LeGall, J., Teixeira, M., Lindley, P., Carrondo, M.A.

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