3ZFS

Cryo-EM structure of the F420-reducing NiFe-hydrogenase from a methanogenic archaeon with bound substrate

Structural Biology Knowledgebase: 3ZFS SBKB.org


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.0 Å
  • Aggregation State: Particle
  • Specimen Type: Vitreous Ice Cryo Em
  • Reconstruction Method: Single Particle

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3ZFS

Classification: OXIDOREDUCTASE

Total Structure Weight: 109136.70

Macromolecule Entities
Molecule Chains Length Organism Details
F420-REDUCING HYDROGENASE, SUBUNIT ALPHA A 405 Methanothermobacter marburgensis EC#: 1.12.98.1 IUBMB
Details: FRHA CONTAINS A NIFE CENTER
Gene Name(s): frhA MTBMA_c16860
F420-REDUCING HYDROGENASE, SUBUNIT GAMMA B 275 Methanothermobacter marburgensis EC#: 1.12.98.1 IUBMB
Details: FRHG CONTAINS THREE 4FE4S CLUSTERS
Gene Name(s): frhG MTBMA_c16840
F420-REDUCING HYDROGENASE, SUBUNIT BETA C 281 Methanothermobacter marburgensis EC#: 1.12.98.1 IUBMB
Details: FRHB CONTAINS FAD AND A 4FE4S CLUSTER
Gene Name(s): frhB MTBMA_c16830

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FAD
Query on FAD

C FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
F42
Query on F42

C COENZYME F420
C29 H36 N5 O18 P
GEHSZWRGPHDXJO-NALJQGANSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

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

A CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

A FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.0 Å
  • Aggregation State: Particle
  • Specimen Type: Vitreous Ice Cryo Em
  • Reconstruction Method: Single Particle

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2012-12-12
  • Released Date: 2013-03-06
  • Deposition author(s): Mills, D.J., Vitt, S., Strauss, M., Shima, S., Vonck, J.

Revision History

  • 2013-04-03
    Type: Citation | Details: JRNL