+Open data
-Basic information
Entry | Database: PDB / ID: 1e9m | ||||||
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Title | Ferredoxin VI from Rhodobacter Capsulatus | ||||||
Components | FERREDOXIN VI | ||||||
Keywords | IRON-SULFUR PROTEIN / FERREDOXIN / [2FE-2S] / BACTERIUM / ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information P450-containing electron transport chain / 2 iron, 2 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | RHODOBACTER CAPSULATUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.07 Å | ||||||
Authors | Sainz, G. / Armengaud, J. / Stojanoff, V. / Sanishvili, N. / Jouanneau, Y. / Larry, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystallization and Preliminary X-Ray Diffraction Analysis of a [2Fe-2S] Ferredoxin (Fdvi) from Rhodobacter Capsulatus Authors: Armengaud, J. / Sainz, G. / Jouanneau, Y. / Sieker, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e9m.cif.gz | 29 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e9m.ent.gz | 21.9 KB | Display | PDB format |
PDBx/mmJSON format | 1e9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/1e9m ftp://data.pdbj.org/pub/pdb/validation_reports/e9/1e9m | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11415.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Strain: B10 / Gene: FDXE / Plasmid: PAJ66 / Gene (production host): FDXE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P80306 |
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#2: Chemical | ChemComp-FES / |
#3: 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: 2.64 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: vapor diffusion / pH: 7.6 Details: 7 M SODIUM FORMATE, IMIDAZOLE PH 7.6, 15 DEG SEEDING IN 3.5-4.2 SODIUM FORMATE. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 288 K / Method: vapor diffusion | ||||||||||||||||||||||||||||||
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: APS / Beamline: 19-ID / Wavelength: 1.741,1.9815 | |||||||||
Detector | Type: ANL-ECT / Detector: CCD / Date: Jul 15, 1999 / Details: MIRROR | |||||||||
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.96→40.161 Å / Num. obs: 16751 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 18.6 Å2 / Rsym value: 0.053 / Net I/σ(I): 24.9 | |||||||||
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.3 / % possible all: 93.7 | |||||||||
Reflection | *PLUS Rmerge(I) obs: 0.053 | |||||||||
Reflection shell | *PLUS % possible obs: 93.7 % / Rmerge(I) obs: 0.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.07→19.27 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 939932.99 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60 Å2 / ksol: 0.399341 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.07→19.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.07→2.2 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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