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- PDB-1ir0: OXIDIZED [4Fe-4S] FERREDOXIN FROM BACILLUS THERMOPROTEOLYTICUS (F... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ir0 | ||||||
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Title | OXIDIZED [4Fe-4S] FERREDOXIN FROM BACILLUS THERMOPROTEOLYTICUS (FORM II) | ||||||
![]() | Ferredoxin | ||||||
![]() | ELECTRON TRANSPORT / FERREDOXIN / IRON-SULFER PROTEIN / ULTLAHIGH RESOLUTION ANALYSIS / GEOMETRY OF [4FE-4S] CLUSTER | ||||||
Function / homology | ![]() 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fukuyama, K. / Okada, T. / Kakuta, Y. / Takahashi, Y. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.7 KB | Display | ![]() |
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PDB format | ![]() | 34.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432 KB | Display | ![]() |
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Full document | ![]() | 431.9 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 9.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1iqzC ![]() 2fxb C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Plasmid: pET21a(+) / Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-SF4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.4 % | ||||||||||||||||||
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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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 21, 2000 |
Radiation | Monochromator: Rotated-inclined double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.55 Å / Relative weight: 1 |
Reflection | Resolution: 1→13.3 Å / Num. all: 35329 / Num. obs: 35329 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1→1.05 Å / Redundancy: 4 % / Rmerge(I) obs: 0.064 / Mean I/σ(I) obs: 9.5 / % possible all: 95.4 |
Reflection | *PLUS Num. measured all: 189925 |
Reflection shell | *PLUS % possible obs: 95.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FXB ![]() 2fxb Resolution: 1→13.3 Å / Num. parameters: 6954 / Num. restraintsaints: 8164 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 506 / Occupancy sum non hydrogen: 744 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→13.3 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: 5.3 % / Rfactor Rwork: 0.096 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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