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- PDB-1iu5: X-ray Crystal Structure of the rubredoxin mutant from Pyrococcus ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1iu5 | ||||||
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Title | X-ray Crystal Structure of the rubredoxin mutant from Pyrococcus Furiosus | ||||||
![]() | rubredoxin | ||||||
![]() | ELECTRON TRANSPORT / rubredoxin / mutant / thermostability | ||||||
Function / homology | ![]() alkane catabolic process / electron transfer activity / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chatake, T. / Kurihara, K. / Tanaka, I. / Tsyba, I. / Bau, R. / Jenney, F.E. / Adams, M.W.W. / Niimura, N. | ||||||
![]() | ![]() Title: A neutron crystallographic analysis of a rubredoxin mutant at 1.6 A resolution. Authors: Chatake, T. / Kurihara, K. / Tanaka, I. / Tsyba, I. / Bau, R. / Jenney, F.E. / Adams, M.W. / Niimura, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22.6 KB | Display | ![]() |
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PDB format | ![]() | 13.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.1 KB | Display | ![]() |
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Full document | ![]() | 417.1 KB | Display | |
Data in XML | ![]() | 4.6 KB | Display | |
Data in CIF | ![]() | 5.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1iu6C ![]() 1brfS 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: 5863.470 Da / Num. of mol.: 1 / Mutation: W3Y, I23V, L32I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-DOD / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.65 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / Details: Na/K phosphate, VAPOR DIFFUSION | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging dropDetails: used macroseeding, Bau, R., (1998) J.BIOL.INORG.CHEM., 3, 484. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: May 29, 2001 |
Radiation | Monochromator: graphite / 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: 8876 / Num. obs: 8876 / % possible obs: 98.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.19 / % possible all: 97.7 |
Reflection | *PLUS Num. measured all: 38773 |
Reflection shell | *PLUS % possible obs: 97.7 % / Rmerge(I) obs: 0.19 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BRF Resolution: 1.5→10 Å / Isotropic thermal model: isotropic / σ(F): 3
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Displacement parameters | Biso mean: 15.9 Å2 | ||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å
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Refinement | *PLUS Lowest resolution: 10 Å / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.189 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |