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Open data
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Basic information
Entry | Database: PDB / ID: 2dxc | ||||||
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Title | Recombinant thiocyanate hydrolase, fully-matured form | ||||||
![]() | (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 | ![]() | 454.3 KB | Display | ![]() |
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PDB format | ![]() | 362.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 548.3 KB | Display | ![]() |
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Full document | ![]() | 579.7 KB | Display | |
Data in XML | ![]() | 100.8 KB | Display | |
Data in CIF | ![]() | 148.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dxbC ![]() 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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Unit cell |
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Details | THE BIOLOGICAL ASSEMBLY IS A DODECAMER AND FOUR EQUIVALENT CATALYTIC CENTERS ARE CONTAINED IN A MOLECULE |
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Components
-Thiocyanate hydrolase subunit ... , 3 types, 12 molecules ADGJBEHKCFIL
#1: Protein | Mass: 14507.152 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 18065.549 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 27619.430 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 3 types, 2539 molecules ![](data/chem/img/3CO.gif)
![](data/chem/img/TLA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TLA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-3CO / #5: Chemical | ChemComp-TLA / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.46 % |
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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: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 6, 2005 Details: Rhodium coated silicon single crystal (Flat shaped, 1000mm(L) x 100mm(W) x 70mm(T)) with 3.5mrad glancing angle |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 269900 / Num. obs: 263483 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 10.8 Å2 / Rsym value: 0.044 |
Reflection shell | Resolution: 1.9→1.97 Å / Rsym value: 0.158 / % possible all: 93.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2DD5 Resolution: 1.9→41.85 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 242999.73 / 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: 49.8588 Å2 / ksol: 0.380175 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→41.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.003 / Total num. of bins used: 6
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Xplor file |
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