+Open data
-Basic information
Entry | Database: PDB / ID: 1r0f | ||||||
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Title | Gallium-substituted rubredoxin | ||||||
Components | Rubredoxin | ||||||
Keywords | ELECTRON TRANSPORT / rubredoxin / Clostridium pasteurianum / iron-sulfur | ||||||
Function / homology | Function and homology information alkane catabolic process / electron transfer activity / iron ion binding Similarity search - Function | ||||||
Biological species | Clostridium pasteurianum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Maher, M. / Cross, M. / Wilce, M.C.J. / Guss, J.M. / Wedd, A.G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Metal-substituted derivatives of the rubredoxin from Clostridium pasteurianum. Authors: Maher, M. / Cross, M. / Wilce, M.C. / Guss, J.M. / Wedd, A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r0f.cif.gz | 23.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r0f.ent.gz | 14.4 KB | Display | PDB format |
PDBx/mmJSON format | 1r0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r0f_validation.pdf.gz | 417.4 KB | Display | wwPDB validaton report |
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Full document | 1r0f_full_validation.pdf.gz | 417.4 KB | Display | |
Data in XML | 1r0f_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 1r0f_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/1r0f ftp://data.pdbj.org/pub/pdb/validation_reports/r0/1r0f | HTTPS FTP |
-Related structure data
Related structure data | 1r0gC 1r0hC 1r0iC 1r0jC 1iroS 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
#1: Protein | Mass: 6051.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00268 |
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#2: Chemical | ChemComp-GA / |
#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: 2.06 Å3/Da / Density % sol: 39.68 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: ammonium sulfate, sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging drop / PH range low: 4.6 / PH range high: 4 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 6611 / Num. obs: 6611 / % possible obs: 99 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 1.6 / Num. unique all: 612 / % possible all: 91.5 |
Reflection | *PLUS Num. measured all: 17349 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 91.5 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1iro Resolution: 1.6→18.57 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.7 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / 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: 15.203 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→18.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 18.7751 Å / Origin y: 25.1253 Å / Origin z: 17.6113 Å
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Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 19 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.206 / Rfactor Rwork: 0.156 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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