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- PDB-1e08: Structural model of the [Fe]-Hydrogenase/cytochrome c553 complex ... -

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Basic information

Entry
Database: PDB / ID: 100000000
TitleStructural model of the [Fe]-Hydrogenase/cytochrome c553 complex combining NMR and soft-docking
Components
  • ([FE]-HYDROGENASE ...) x 2
  • CYTOCHROME C553
KeywordsHYDROGENASE / CYTOCHROME C553 / ELECTRON TRANSFER COMPLEX
Function / homology
Function and homology information


ferredoxin hydrogenase / 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 / Iron hydrogenase, small subunit superfamily / 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 ...Iron hydrogenase, small subunit HydB-type / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit superfamily / 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 / 4Fe-4S binding domain / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain 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 c-553 / Periplasmic [Fe] hydrogenase large subunit / Periplasmic [Fe] hydrogenase small subunit
Similarity search - Component
Biological speciesDESULFOVIBRIO DESULFURICANS (bacteria)
DESULFOVIBRIO VULGARIS (bacteria)
MethodSOLUTION NMR / THEORETICAL MODEL
Model type detailsMINIMIZED AVERAGE
AuthorsMorelli, X. / Czjzek, M. / Hatchikian, C.E. / Bornet, O. / Fontecilla-Camps, J.C. / Palma, N.P. / Moura, J.J.G. / Guerlesquin, F.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Structural Model of the Fe-Hydrogenase/Cytochrome C553 Complex Combining Transverse Relaxation-Optimized Spectroscopy Experiments and Soft Docking Calculations.
Authors: Morelli, X. / Czjzek, M. / Hatchikian, C.E. / Bornet, O. / Fontecilla-Camps, J.C. / Palma, N.P. / Moura, J.J. / Guerlesquin, F.
#1: Journal: Biochemistry / Year: 2000
Title: Heteronuclear NMR and Soft Docking: An Experimental Approach for a Structural Model of the Cytochrome C553-Ferredoxin Complex
Authors: Morelli, X. / Dolla, A. / Czjzek, M. / Palma, P.N. / Blasco, F. / Krippahl, L. / Moura, J.J.G.
History
DepositionMar 13, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 21, 2019Group: Data collection / Derived calculations / Category: pdbx_nmr_software / struct_conn
Item: _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Sep 25, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_database_status.status_code_mr / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Nov 27, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: [FE]-HYDROGENASE (LARGE SUBUNIT)
D: [FE]-HYDROGENASE (SMALL SUBUNIT)
E: CYTOCHROME C553
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,63515
Polymers58,5683
Non-polymers2,06712
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1000LEAST SHIFT VARIATION VIOLATION
Representative

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Components

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

#1: Protein [FE]-HYDROGENASE (LARGE SUBUNIT)


Mass: 40239.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO DESULFURICANS (bacteria) / Cellular location: PERIPLASM / References: UniProt: P07598*PLUS
#2: Protein [FE]-HYDROGENASE (SMALL SUBUNIT)


Mass: 10082.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO DESULFURICANS (bacteria) / Cellular location: PERIPLASM / References: UniProt: P07603*PLUS

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Protein , 1 types, 1 molecules E

#3: Protein CYTOCHROME C553


Mass: 8246.454 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Cellular location: PERIPLASM / Strain: HILDENBOROUGH / References: UniProt: P04032*PLUS

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Non-polymers , 8 types, 13 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#10: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINAL END C-TERMINAL RESIDUES WERE NOT DEPOSITED IN THE INITIAL PDB ENTRY 1HFE TER ALA: THE C- ...N-TERMINAL END C-TERMINAL RESIDUES WERE NOT DEPOSITED IN THE INITIAL PDB ENTRY 1HFE TER ALA: THE C-TERMINAL RESIDUES 398-421 ARE NOT PRESENT IN THE PDB FILE OF HYDROGENASE 1HFE

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
THEORETICAL MODEL
NMR experimentType: TROSY
NMR detailsText: COMBINED DOCKING AND NMR FILTERING SOLUTION. THE TROSY EXPERIMENT WAS PERFORMED ON THE 15N-LABELED CYTOCHROME WITH SUBSEQUENTLY ADDING OF THE HYDROGENASE. THE RESIDUES HAVING THE STRONGEST ...Text: COMBINED DOCKING AND NMR FILTERING SOLUTION. THE TROSY EXPERIMENT WAS PERFORMED ON THE 15N-LABELED CYTOCHROME WITH SUBSEQUENTLY ADDING OF THE HYDROGENASE. THE RESIDUES HAVING THE STRONGEST SHIFTS WERE USED TO FILTER THE DOCKING SOLUTIONS.THE AMINO-ACIDS ALA E5, CYS E10, HIS E14, GLY E15, ALA E16, ALA E22, GLY E24, VAL E29, GLN E32, LYS E54, ASN E59, ALA E60 OF THE CYTOCHROME C553 SHOW STRONGEST SHIFTS IN THE TROSY EXPERIMENTS. EACH TIME ONE OF THE AMINO ACIDS IS IN CONTACT (LESS THAN 5A IN THE COMPLEX) WITH ITS PARTNER ONE POINT IS ATTRIBUTED TO THE STRUCTURE. THEN THE ONE THOUSAND BEST STRUCTURES ARE RANKED ACCORDING TO THIS CRITERIUM AND THE 10 BEST SOLUTIONS ARE MINIMISED. A COMPARISON OF THESE SOLUTIONS GENERATES STRUCTURE WITH 5 IDENTICAL SOLUTIONS

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Sample preparation

DetailsContents: 10% D2O/90% WATER
Sample conditionsIonic strength: 10MM TRIS/HCL / pH: 7.6 / Pressure: 1 atm / Temperature: 296 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Data collection

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.843BRUNGERrefinement
UXNMRUXNMRstructure solution
RefinementSoftware ordinal: 1
Details: THE DEPOSITED STRUCTURE IS THE RESULT OF A HETERONUCLEAR NMR EXPERIMENT AND DOCKING SIMULATIONS. THE FINAL RESULT WAS MINIMIZED BY MOLECULAR DYNAMIC MINIMIZATION.
NMR ensembleConformer selection criteria: LEAST SHIFT VARIATION VIOLATION
Conformers calculated total number: 1000 / Conformers submitted total number: 1

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