6HUY

HmdII from Desulfurobacterium thermolithotrophum reconstitued with Fe-guanylylpyridinol (FeGP) cofactor and co-crystallized with methenyl-tetrahydrofolate form A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The bacterial [Fe]-hydrogenase paralog uses tetrahydrofolate derivatives as substrates.

Watanabe, T.Wagner, T.Huang, G.Kahnt, J.Ataka, K.Ermler, U.Shima, S.

(2019) Angew. Chem. Int. Ed. Engl. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coenzyme F420-dependent N(5),N(10)-methenyltetrahydromethanopterin reductase-related protein
A, C
370Desulfurobacterium thermolithotrophum (strain DSM 11699 / BSA)Mutation(s): 0 
Find proteins for F0S2B6 (Desulfurobacterium thermolithotrophum (strain DSM 11699 / BSA))
Go to UniProtKB:  F0S2B6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coenzyme F420-dependent N(5),N(10)-methenyltetrahydromethanopterin reductase-related protein
B, D
370Desulfurobacterium thermolithotrophum (strain DSM 11699 / BSA)Mutation(s): 0 
Find proteins for F0S2B6 (Desulfurobacterium thermolithotrophum (strain DSM 11699 / BSA))
Go to UniProtKB:  F0S2B6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GUE
Query on GUE

Download SDF File 
Download CCD File 
A, B, C, D
5,10-Methenyltetrahydrofolate
C20 H22 N7 O6
MEANFMOQMXYMCT-OLZOCXBDSA-O
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
FE9
Query on FE9

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Download CCD File 
A, C
iron-guanylyl pyridinol cofactor
C21 H23 Fe N6 O13 P S
AEHOAZNVUAGELD-VPXBKTNXSA-K
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
B, C, D
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
B, D
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 99.769α = 90.00
b = 131.829β = 90.00
c = 168.263γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
Ministry of Education (China)China--

Revision History 

  • Version 1.0: 2019-01-09
    Type: Initial release