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- PDB-2zzd: Recombinant thiocyanate hydrolase, air-oxidized form of holo-enzyme -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zzd | ||||||
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Title | Recombinant thiocyanate hydrolase, air-oxidized form of holo-enzyme | ||||||
![]() | (Thiocyanate hydrolase subunit ...) x 3 | ||||||
![]() | HYDROLASE / SCNASE / 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 / CYSTEINE / OXIDATION / AUTOCATALYTIC ACTIVATION / AIR INACTIVATION / Metal-binding | ||||||
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 | ![]() | 478.7 KB | Display | ![]() |
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PDB format | ![]() | 383 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 576.2 KB | Display | ![]() |
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Full document | ![]() | 598.5 KB | Display | |
Data in XML | ![]() | 110.3 KB | Display | |
Data in CIF | ![]() | 166 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dxbC ![]() 2dxcC ![]() 2dd5S S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Details | THE BIOLOGICAL ASSEMBLY IS A SCNASE DODECAMERIC COMPLEX 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: 27635.428 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/FRU.gif)
![](data/chem/img/BGC.gif)
![](data/chem/img/BGC.gif)
#4: Sugar | #7: Sugar | ChemComp-BGC / | |
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-Non-polymers , 3 types, 3410 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)
#5: Chemical | ChemComp-3CO / #6: Chemical | ChemComp-TLA / #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | THIS PROTEIN CATALYZES THE PRODUCTION |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.56 % |
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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 4 / Detector: CCD / Date: Mar 10, 2006 / Details: Mirror: 11.8m x 1.1m long bent plane mirror of ULE |
Radiation | Monochromator: 14.5m Triangular Si(111) with an asymmetric angle of 7.8 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. all: 327300 / Num. obs: 319150 / % possible obs: 97.3 % / Observed criterion σ(I): 1.5 / Redundancy: 5.3 % / Biso Wilson estimate: 15.8 Å2 / Rsym value: 0.051 / Net I/σ(I): 13.9 / Num. measured all: 1677550 |
Reflection shell | Resolution: 1.78→1.84 Å / Redundancy: 5.1 % / Num. unique all: 30773 / Rsym value: 0.29 / % possible all: 94.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2DD5 Resolution: 1.78→40.76 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 54162.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.5298 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.78→40.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.89 Å / Rfactor Rfree error: 0.003 / Total num. of bins used: 6
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Xplor file |
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