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- PDB-2dxb: Recombinant thiocyanate hydrolase comprising partially-modified c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dxb | ||||||
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Title | Recombinant thiocyanate hydrolase comprising partially-modified cobalt centers | ||||||
![]() | (Thiocyanate hydrolase subunit ...) x 3 | ||||||
![]() | HYDROLASE / cobalt / metalloprotein / sulfenic acid / sulfinic acid / nitrile hydratase / thiocyanate / carbonyl sulfide / claw setting / protein / enzyme / complex / model complex / non-corrin / post-translational modification / sulfenate / sulfinate | ||||||
Function / homology | ![]() thiocyanate hydrolase / thiocyanate hydrolase activity / thiocyanate catabolic process / transition metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Arakawa, T. / Kawano, Y. / Katayama, Y. / Yohda, M. / Odaka, M. | ||||||
![]() | ![]() Title: Structural Basis for Catalytic Activation of Thiocyanate Hydrolase Involving Metal-Ligated Cysteine Modification Authors: Arakawa, T. / Kawano, Y. / Katayama, Y. / Nakayama, H. / Dohmae, N. / Yohda, M. / Odaka, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 824.7 KB | Display | ![]() |
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PDB format | ![]() | 675.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 623.3 KB | Display | ![]() |
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Full document | ![]() | 674 KB | Display | |
Data in XML | ![]() | 168.2 KB | Display | |
Data in CIF | ![]() | 237 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dxcC ![]() 2zzdC ![]() 2dd5S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | THE BIOLOGICAL ASSEMBLY IS A DODECAMER (CHAIN A-L AND M-X OF THIS RECORD) AND FOUR EQUIVALENT CATALYTIC CENTERS ARE CONTAINED IN A MOLECULE |
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Components
-Thiocyanate hydrolase subunit ... , 3 types, 24 molecules ADGJMPSVBEHKNQTWCFILORUX
#1: Protein | Mass: 14507.152 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 18065.549 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 27619.430 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 3 types, 2957 molecules ![](data/chem/img/3CO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-3CO / #5: Chemical | ChemComp-PO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 1.5M Na/K Tartrate, 0.1M Potassium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 10, 2004 |
Radiation | Monochromator: Diamond crystals; First crystal is in Laue setting, and second one is in Bragg setting Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 324000 / Num. obs: 322968 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 11.3 Å2 / Rsym value: 0.099 / Net I/σ(I): 0.085 |
Reflection shell | Resolution: 2.25→2.33 Å / Rsym value: 0.208 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2DD5 Resolution: 2.25→49.41 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 327805.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.419 Å2 / ksol: 0.393681 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→49.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.003 / Total num. of bins used: 6
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Xplor file |
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