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Open data
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Basic information
Entry | Database: PDB / ID: 1r0i | ||||||
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Title | cadmium-substituted rubredoxin | ||||||
![]() | Rubredoxin | ||||||
![]() | ELECTRON TRANSPORT / rubredoxin / iron-sulfur / Clostridium pasteurianum | ||||||
Function / homology | ![]() alkane catabolic process / electron transfer activity / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Maher, M. / Cross, M. / Wilce, M.C.J. / Guss, J.M. / Wedd, A.G. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 23.4 KB | Display | ![]() |
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PDB format | ![]() | 14.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 407.9 KB | Display | ![]() |
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Full document | ![]() | 407.9 KB | Display | |
Data in XML | ![]() | 4.6 KB | Display | |
Data in CIF | ![]() | 5.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1r0fC ![]() 1r0gC ![]() 1r0hC ![]() 1r0jC ![]() 1iroS 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
#1: Protein | Mass: 6051.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 37.7 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: sodium acetate, ammonium sulfate, 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: ![]() |
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: 1.5→50 Å / Num. all: 7544 / Num. obs: 7544 / % possible obs: 93.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 14.5 |
Reflection shell | Highest resolution: 1.5 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 1.5 / % possible all: 66.4 |
Reflection | *PLUS Num. measured all: 29513 |
Reflection shell | *PLUS % possible obs: 66.4 % / Rmerge(I) obs: 0.12 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1iro Resolution: 1.5→18.57 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.991 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The Rfree set was correctly assigned. The R(work) and R(free) values were 0.315 and 0.348, respectively at the commencement of the ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The Rfree set was correctly assigned. The R(work) and R(free) values were 0.315 and 0.348, respectively at the commencement of the refinement. They converged during the refinement. Author has no explanation as to why the value for R(free) is lower than that for R(work).
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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: 14.633 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→18.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.502→1.54 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 18.9662 Å / Origin y: 25.184 Å / Origin z: 17.9664 Å
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Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 19 Å / Num. reflection obs: 7541 / % reflection Rfree: 5 % / Rfactor Rfree: 0.146 / Rfactor Rwork: 0.146 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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