6H63

Semisynthetic [FeFe]-hydrogenase CpI with ethanedithiolate [2Fe] cofactor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Geometry of the Catalytic Active Site in [FeFe]-Hydrogenase Is Determined by Hydrogen Bonding and Proton Transfer

Duan, J.Mebs, S.Laun, K.Wittkamp, F.Heberle, J.Happe, T.Hofmann, E.Apfel, U.-P.Winkler, M.Senger, M.Haumann, M.Stripp, S.

(2019) ACS Catal 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Iron hydrogenase 1A, B584Clostridium pasteurianumMutation(s): 0 
EC: 1.12.7.2
UniProt
Find proteins for P29166 (Clostridium pasteurianum)
Explore P29166 
Go to UniProtKB:  P29166
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29166
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
L [auth B],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FU8
Query on FU8

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
dicarbonyl[bis(cyanide-kappaC)]-mu-(ethanethiolatato-1kappaS:2kappaS)-mu-(ox omethylidene)diiron(2+)
C7 H4 Fe2 N2 O3 S2
MZEMAHMYMVUPIF-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
H [auth A],
P [auth B]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
Q [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.02α = 90
b = 73.53β = 97.66
c = 104.14γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Data collection