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- PDB-1gx7: Best model of the electron transfer complex between cytochrome c3... -

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Basic information

Entry
Database: PDB / ID: 1gx7
TitleBest model of the electron transfer complex between cytochrome c3 and [Fe]-hydrogenase
Components
  • (PERIPLASMIC [FE] HYDROGENASE ...) x 2
  • CYTOCHROME C3
KeywordsOXIDOREDUCTASE / ELECTRON TRANSFER COMPLEX / HYDROGENASE / MULTIHEME CYTOCHROME / SOFT DOCKING / OXIDOREDUCTASE ELECTRON TRANSPORT / 4FE-4S / IRON-SULFUR
Function / homology
Function and homology information


ferredoxin hydrogenase / anaerobic respiration / ferredoxin hydrogenase activity / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / periplasmic space / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Iron hydrogenase, small subunit HydB-type / 4Fe-4S dicluster domain / Class III cytochrome C / Iron hydrogenase, small subunit superfamily / Class III cytochrome C family / Iron hydrogenase, subset / Iron hydrogenase, small subunit / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal ...Iron hydrogenase, small subunit HydB-type / 4Fe-4S dicluster domain / Class III cytochrome C / Iron hydrogenase, small subunit superfamily / Class III cytochrome C family / Iron hydrogenase, subset / Iron hydrogenase, small subunit / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / Cytochrome c, class III / Multiheme cytochrome c family profile. / 4Fe-4S binding domain / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Multiheme cytochrome superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
CARBON MONOXIDE / CYANIDE ION / : / HEME C / 1,3-PROPANEDITHIOL / IRON/SULFUR CLUSTER / Cytochrome c3 / Periplasmic [Fe] hydrogenase large subunit / Periplasmic [Fe] hydrogenase small subunit
Similarity search - Component
Biological speciesDESULFOVIBRIO VULGARIS (bacteria)
MethodSOLUTION NMR / THEORETICAL MODEL
Model type detailsMINIMIZED AVERAGE
AuthorsElantak, L. / Morelli, X. / Bornet, O. / Hatchikian, C. / Czjzek, M. / Dolla, A. / Guerlesquin, F.
CitationJournal: FEBS Lett. / Year: 2003
Title: The Cytochrome C(3)-[Fe]-Hydrogenase Electron-Transfer Complex: Structural Model by NMR Restrained Docking
Authors: Elantak, L. / Morelli, X. / Bornet, O. / Hatchikian, C. / Czjzek, M. / Dolla, A. / Guerlesquin, F.
History
DepositionMar 28, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: pdbx_nmr_spectrometer
Item: _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 1.4Aug 21, 2019Group: Data collection / Derived calculations / Category: pdbx_nmr_software / struct_conn
Item: _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 27, 2019Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PERIPLASMIC [FE] HYDROGENASE LARGE SUBUNIT
D: PERIPLASMIC [FE] HYDROGENASE SMALL SUBUNIT
E: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,86617
Polymers62,0093
Non-polymers3,85714
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

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PERIPLASMIC [FE] HYDROGENASE ... , 2 types, 2 molecules AD

#1: Protein PERIPLASMIC [FE] HYDROGENASE LARGE SUBUNIT


Mass: 40239.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: P07598, 1.18.99.1
#2: Protein PERIPLASMIC [FE] HYDROGENASE SMALL SUBUNIT


Mass: 10082.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: P07603, 1.18.99.1

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Protein , 1 types, 1 molecules E

#3: Protein CYTOCHROME C3


Mass: 11687.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: P00131

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Non-polymers , 6 types, 14 molecules

#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-PDT / 1,3-PROPANEDITHIOL / Propane-1,3-dithiol


Mass: 108.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8S2
#6: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#7: Chemical ChemComp-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#8: Chemical ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#9: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
THEORETICAL MODEL
NMR experimentType: HSQC
NMR detailsText: THE COMPLEX MODEL WAS DETERMINED WITH NMR-RESTRAINED (HSQC) SOFT DOCKING, THEN MINIMIZED BY MOLECULAR DYNAMICS

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Sample preparation

Sample conditionsIonic strength: 10 MM PHOSPHATE BUFFER / pH: 5.9 / Pressure: 1 atm / Temperature: 296 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX5002

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Processing

NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
RefinementSoftware ordinal: 1
Details: A MOLECULAR DYNAMICS CALCULATION (AMBER FORCE FIELD) WITH SHAKE RESTRAINTS FOR THE HETEROATOMS WAS PERFORMED HEAT-BATH TEMPERATURE: 280 K INITIAL VELOCITIES FROM A MAXWELL-BOLTZMAN ...Details: A MOLECULAR DYNAMICS CALCULATION (AMBER FORCE FIELD) WITH SHAKE RESTRAINTS FOR THE HETEROATOMS WAS PERFORMED HEAT-BATH TEMPERATURE: 280 K INITIAL VELOCITIES FROM A MAXWELL-BOLTZMAN DISTRIBUTION AT 280K. SHAKE RESTRAINTS WITH A TOLERANCE OF 0.0004. THIS IS A MODEL COMPLEX OBTAINED BY NMR-RESTRAINED SOFT DOCKING AND MINIMIZATION.
NMR ensembleConformers submitted total number: 1

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