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Yorodumi- PDB-1dwl: The Ferredoxin-Cytochrome complex using heteronuclear NMR and doc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dwl | ||||||
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Title | The Ferredoxin-Cytochrome complex using heteronuclear NMR and docking simulation | ||||||
Components |
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Keywords | ELECTRON TRANSFER / FERREDOXIN-CYTOCHROME COMPLEX / MODEL / HETERONUCLEAR NMR / DOCKING | ||||||
Function / homology | Function and homology information 4 iron, 4 sulfur cluster binding / electron transfer activity / periplasmic space / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | DESULFOMICROBIUM NORVEGICUM (bacteria) DESULFOVIBRIO VULGARIS (bacteria) | ||||||
Method | SOLUTION NMR / THEORETICAL MODEL / MAPPING OF THE CHEMICAL SHIFT VARIATIONS | ||||||
Model details | MODELLING 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 | ||||||
Authors | Morelli, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dwl.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dwl.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 1dwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/1dwl ftp://data.pdbj.org/pub/pdb/validation_reports/dw/1dwl | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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#2: Protein | 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 / |
#4: Chemical | ChemComp-HEC / |
-Experimental details
-Experiment
Experiment |
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NMR experiment | Type: HSQC | |||
NMR details | Text: HETERONUCLEAR EXPERIMENTS ON 15N-LABELED FERREDOXIN AND CYTOCHROME, CHEMICAL SHIFT VARIATION ANALYSIS |
-Sample preparation
Details | Contents: 10% D2O/90% WATER |
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Sample conditions | pH: 5.9 / Temperature: 296 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-Data collection
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
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-Processing
NMR software | Name: X-PLOR / Version: 3.851 / Developer: BRUNGER / Classification: refinement |
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Refinement | Method: 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 ensemble | Conformer selection criteria: COMBINATION OF NMR SHIFT VARIATION AND A SOFT DOCKING ALGORITHM Conformers submitted total number: 3 |