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Yorodumi- PDB-1siz: Crystal structure of the [Fe3S4]-ferredoxin from the hyperthermop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1siz | ||||||
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Title | Crystal structure of the [Fe3S4]-ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus | ||||||
Components | Ferredoxin | ||||||
Keywords | ELECTRON TRANSPORT / thermostability / iron-sulfur clusters / dimer | ||||||
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: 2.25 Å | ||||||
Authors | Nielsen, M.S. / Harris, P. / Christensen, H.E.M. | ||||||
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 | 1siz.cif.gz | 38.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1siz.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 1siz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1siz_validation.pdf.gz | 386.1 KB | Display | wwPDB validaton report |
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Full document | 1siz_full_validation.pdf.gz | 386.9 KB | Display | |
Data in XML | 1siz_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 1siz_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/1siz ftp://data.pdbj.org/pub/pdb/validation_reports/si/1siz | HTTPS FTP |
-Related structure data
Related structure data | 1sj1C 1vjwS C: citing same article (ref.) 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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Details | The biological assembly is either the dimer in the asymmetric unit or a monomer |
-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-3CO / #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: 2.33 Å3/Da / Density % sol: 47.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 400, hexammine cobalt(III)-ions, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9999 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 17, 2003 |
Radiation | Monochromator: Silicium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→35 Å / Num. obs: 6508 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 28.06 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.25→2.37 Å / Rmerge(I) obs: 0.22 / % possible all: 81.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1VJW Resolution: 2.25→35 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.25→35 Å
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Refine LS restraints |
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