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Yorodumi- PDB-1sj1: The 1.5 A Resolution Crystal Structure of [Fe3S4]-Ferredoxin from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sj1 | ||||||
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Title | The 1.5 A Resolution Crystal Structure of [Fe3S4]-Ferredoxin from the hyperthermophilic Archaeon Pyrococcus furiosus | ||||||
Components | Ferredoxin | ||||||
Keywords | ELECTRON TRANSPORT / thermostability / iron-sulfur cluster / hexammine cobalt(III) | ||||||
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: 1.5 Å | ||||||
Authors | Nielsen, M.S. / Harris, P. / Ooi, B.L. / Christensen, H.E. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: The 1.5 A Resolution Crystal Structure of [Fe3S4]-Ferredoxin from the Hyperthermophilic Archaeon Pyrococcus furiosus Authors: Nielsen, M.S. / Harris, P. / Ooi, B.L. / Christensen, H.E.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sj1.cif.gz | 40.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sj1.ent.gz | 32.4 KB | Display | PDB format |
PDBx/mmJSON format | 1sj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sj1_validation.pdf.gz | 470.1 KB | Display | wwPDB validaton report |
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Full document | 1sj1_full_validation.pdf.gz | 474.3 KB | Display | |
Data in XML | 1sj1_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 1sj1_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/1sj1 ftp://data.pdbj.org/pub/pdb/validation_reports/sj/1sj1 | HTTPS FTP |
-Related 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: 7171.001 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: FDXA, PF1909 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P29603 #2: Chemical | ChemComp-NCO / #3: Chemical | #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: 2.61 Å3/Da / Density % sol: 52.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 400, hexammine cobalt(III)chloride, Tris/HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 2, 2003 |
Radiation | Monochromator: Silicium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→34.6 Å / Num. obs: 21276 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.31 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→50.64 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.872 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.634 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→50.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20 /
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