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Yorodumi- PDB-4dhv: Crystal structure of the Pyrococcus furiosus ferredoxin D14C vari... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dhv | ||||||
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Title | Crystal structure of the Pyrococcus furiosus ferredoxin D14C variant containing the heterometallic [AgFe3S4] cluster | ||||||
Components | Ferredoxin | ||||||
Keywords | ELECTRON TRANSPORT / ferredoxin / Pyrococcus furiosus / iron-sulfur protein / heterometallic / [AgFe3S4] cluster / silver / artificial metalloprotein | ||||||
Function / homology | Function and homology information 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Jakab-Simon, I.N. / Christensen, H.E.M. / Haahr, L.T. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2013 Title: Heterometallic [AgFe(3)S (4)] ferredoxin variants: synthesis, characterization, and the first crystal structure of an engineered heterometallic iron-sulfur protein. Authors: Martic, M. / Jakab-Simon, I.N. / Haahr, L.T. / Hagen, W.R. / Christensen, H.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dhv.cif.gz | 43.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dhv.ent.gz | 29.7 KB | Display | PDB format |
PDBx/mmJSON format | 4dhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/4dhv ftp://data.pdbj.org/pub/pdb/validation_reports/dh/4dhv | HTTPS FTP |
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-Related structure data
Related structure data | 2z8qS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7159.056 Da / Num. of mol.: 2 / Mutation: D14C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM3638 / Gene: fdxA, Ferredoxin, PF1909 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29603 #2: Chemical | #3: Chemical | ChemComp-NCO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.8 % |
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Crystal grow | Temperature: 277 K / pH: 7.5 Details: PEG600, malonic acid/imidazol/boric acid buffer mixture, [Co(NH3)6]Cl3, pH 7.5, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.97918 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 3, 2011 |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→25 Å / Num. obs: 16141 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.63 |
Reflection shell | Resolution: 1.95→2.07 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2.13 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z8Q Resolution: 1.95→24.66 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.883 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.862 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.88 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→24.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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