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- PDB-1dwl: The Ferredoxin-Cytochrome complex using heteronuclear NMR and doc... -

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Basic information

Entry
Database: PDB / ID: 1dwl
TitleThe Ferredoxin-Cytochrome complex using heteronuclear NMR and docking simulation
Components
  • CYTOCHROME C553
  • FERREDOXIN I
KeywordsELECTRON TRANSFER / FERREDOXIN-CYTOCHROME COMPLEX / MODEL / HETERONUCLEAR NMR / DOCKING
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
: / 3Fe-4S ferredoxin / 4Fe-4S single cluster domain of Ferredoxin I / 4Fe-4S binding domain / 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. ...: / 3Fe-4S ferredoxin / 4Fe-4S single cluster domain of Ferredoxin I / 4Fe-4S binding domain / 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. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
HEME C / IRON/SULFUR CLUSTER / Cytochrome c-553 / Ferredoxin-1
Similarity search - Component
Biological speciesDESULFOMICROBIUM NORVEGICUM (bacteria)
DESULFOVIBRIO VULGARIS (bacteria)
MethodSOLUTION NMR / THEORETICAL MODEL / MAPPING OF THE CHEMICAL SHIFT VARIATIONS
Model detailsMODELLING EXPERIMENT: THE COMPLEX STRUCTURE WAS OBTAINED BY SOFT DOCKING ALGORITHM IMPLEMENTED WITH ...MODELLING EXPERIMENT: THE COMPLEX STRUCTURE WAS OBTAINED BY SOFT DOCKING ALGORITHM IMPLEMENTED WITH AN NMR FILTER. THE STARTING MODELS OF THE CYTOCHROME AND THE FERREDOXIN WERE BASED ON THE PDB ENTRIES 1DVH AND 1FXD
AuthorsMorelli, X. / Guerlesquin, F. / Czjzek, M. / Palma, P.N.
Citation
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. / Guerlesquin, F.
#1: Journal: Proteins: Struct.,Funct., Genet. / Year: 2000
Title: Bigger: A New (Soft) Docking Algorithm for Predicting Protein Interactions
Authors: Palma, P.N. / Krippahl, L. / Wampler, J.E. / Moura, J.J.G.
#2: Journal: FEBS Lett. / Year: 1999
Title: Mapping the Cytochrome C553 Interacting Site Using 1H and 15N NMR
Authors: Morelli, X. / Guerlesquin, F.
History
DepositionDec 8, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 1999Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERREDOXIN I
B: CYTOCHROME C553
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5524
Polymers14,5822
Non-polymers9702
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)3 / -COMBINATION OF NMR SHIFT VARIATION AND A SOFT DOCKING ALGORITHM
RepresentativeModel #2

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Components

#1: Protein FERREDOXIN I


Mass: 6264.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CONTAINS A FE4S4 CLUSTER COVALENTLY LINKED BY FOUR CYSTEINS
Source: (gene. exp.) DESULFOMICROBIUM NORVEGICUM (bacteria) / Cellular location: PERIPLASM / Gene: FDXI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P07485
#2: Protein CYTOCHROME C553 / LOW POTENTIAL CYTOCHROME C


Mass: 8317.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CONTAINS A HEME GROUP COVALENTLY LINKED BY 2 CYSTEINES AND THE IRON ATOM IS COORDINATED BY A HISTIDINE AND A METHIONINE
Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Cellular location: CYTOPLASM / Strain: HILDENBOROUGH / References: UniProt: P04032
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
Has protein modificationY

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
THEORETICAL MODEL
NMR experimentType: HSQC
NMR detailsText: HETERONUCLEAR EXPERIMENTS ON 15N-LABELED FERREDOXIN AND CYTOCHROME, CHEMICAL SHIFT VARIATION ANALYSIS

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Sample preparation

DetailsContents: 10% D2O/90% WATER
Sample conditionspH: 5.9 / 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 softwareName: X-PLOR / Version: 3.851 / Developer: BRUNGER / Classification: refinement
RefinementMethod: MAPPING OF THE CHEMICAL SHIFT VARIATIONS / Software ordinal: 1
Details: MOLECULAR DYNAMICS CALCULATION USING AMBER FORCE FIELD THESE ARE 3 MODEL STRUCTURES FOR THE COMPLEX OF CYTOCHROME C553 WITH FERREDOXIN I
NMR ensembleConformer selection criteria: COMBINATION OF NMR SHIFT VARIATION AND A SOFT DOCKING ALGORITHM
Conformers submitted total number: 3

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