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Yorodumi- PDB-1iqz: OXIDIZED [4Fe-4S] FERREDOXIN FROM BACILLUS THERMOPROTEOLYTICUS (F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iqz | |||||||||
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Title | OXIDIZED [4Fe-4S] FERREDOXIN FROM BACILLUS THERMOPROTEOLYTICUS (FORM I) | |||||||||
Components | Ferredoxin | |||||||||
Keywords | ELECTRON TRANSPORT / FERREDOXIN / IRON-SULFER PROTEIN / ULTLAHIGH RESOLUTION ANALYSIS / GEOMETRY OF [4FE-4S] CLUSTER | |||||||||
Function / homology | Function and homology information 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding Similarity search - Function | |||||||||
Biological species | Bacillus thermoproteolyticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.92 Å | |||||||||
Authors | Fukuyama, K. / Okada, T. / Kakuta, Y. / Takahashi, Y. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Atomic resolution structures of oxidized [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus in two crystal forms: systematic distortion of [4Fe-4S] cluster in the protein. Authors: Fukuyama, K. / Okada, T. / Kakuta, Y. / Takahashi, Y. #1: Journal: J.Mol.Biol. / Year: 1989 Title: Structure of [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus refined at 2.3 A resolution. Structural comparisons of bacterial ferredoxins. Authors: Fukuyama, K. / Matsubara, H. / Tsukihara, T. / Katsube, Y. #2: Journal: J.Mol.Biol. / Year: 1988 Title: Tertiary structure of Bacillus thermoproteolyticus [4Fe-4S] ferredoxin. Evolutionary implications for bacterial ferredoxins. Authors: Fukuyama, K. / Nagahara, Y. / Tsukihara, T. / Katsube, Y. / Hase, T. / Matsubara, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iqz.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iqz.ent.gz | 37.2 KB | Display | PDB format |
PDBx/mmJSON format | 1iqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/1iqz ftp://data.pdbj.org/pub/pdb/validation_reports/iq/1iqz | HTTPS FTP |
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-Related structure data
Related structure data | 1ir0C 2fxb 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 8773.595 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thermoproteolyticus (bacteria) Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P10245 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-SF4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.7 % | ||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: microdialysis / pH: 6.5 Details: ammonium sulfate, MES, pH 6.5, MICRODIALYSIS, temperature 277.0K | ||||||||||||||||||
Crystal grow | *PLUS PH range low: 7.2 / PH range high: 6.5 | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.7 / Wavelength: 0.7 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2000 / Details: BENT CYLINDER |
Radiation | Monochromator: FIXED-EXIT DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 0.92→13.5 Å / Num. all: 54415 / Num. obs: 54415 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 0.92→0.96 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 2.7 / % possible all: 99.5 |
Reflection | *PLUS Num. measured all: 265846 |
Reflection shell | *PLUS % possible obs: 99.5 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2FXB 2fxb Resolution: 0.92→7 Å / Num. parameters: 7323 / Num. restraintsaints: 8708 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 486 / Occupancy sum non hydrogen: 766 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.92→7 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.5 % / Rfactor all: 0.098 / Rfactor Rfree: 0.11 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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