1NFV

X-ray structure of Desulfovibrio desulfuricans bacterioferritin: the diiron centre in different catalytic states (as-isolated structure)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.214

Literature

Macromolecules
Sequence Display for 1NFV

Classification: IRON STORAGE / ELECTRON TRANSPORT

Total Structure Weight: 333169.38

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

B, D, F, 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)
3PY
Query on 3PY

D 3-HYDROXYPYRUVIC ACID
C3 H4 O4
HHDDCCUIIUWNGJ-UHFFFAOYSA-N
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)
GOL
Query on GOL

A, B, C, D, E, F, G, H, I, J, K, M, N, O, P GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.214
  • Space Group: P 21 3

Unit Cell:

Length (Å) Angle (°)
a = 225.30 α = 90.00
b = 225.30 β = 90.00
c = 225.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-12-16
  • 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

  • Version 1_0: 2003-04-01

    Type: Initial release

  • Version 1_1: 2008-05-02

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Derived calculations, Version format compliance

  • Version 1_3: 2017-10-11

    Type: Refinement description