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Open data
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Basic information
Entry | Database: PDB / ID: 7akn | ||||||
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Title | Thermolysin from Bacillus thermoproteolyticus | ||||||
![]() | Thermolysin | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boikova, A.S. / Ilina, K.B. / Marchenkova, M.A. / Pisarevsky, Y.V. / Timofeev, V.I. / Kovalchuk, M.V. | ||||||
![]() | ![]() Title: Thermolysin from Bacillus thermoproteolyticus Authors: Boikova, A.S. / Ilina, K.B. / Marchenkova, M.A. / Pisarevsky, Y.V. / Timofeev, V.I. / Kovalchuk, M.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.2 KB | Display | ![]() |
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PDB format | ![]() | 57.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.3 KB | Display | ![]() |
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Full document | ![]() | 449.3 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1keiS 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: npr / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 112 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/VAL.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/VAL.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-VAL / | #5: Chemical | ChemComp-LYS / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→30 Å / Num. obs: 12427 / % possible obs: 99.79 % / Redundancy: 6.14 % / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.074 / Net I/σ(I): 8.9885 |
Reflection shell | Resolution: 2.46→2.59 Å / Rmerge(I) obs: 0.35 / Num. unique obs: 1769 / Rrim(I) all: 0.47 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KEI Resolution: 2.46→29.98 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.445 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.518 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.68 Å2 / Biso mean: 38.663 Å2 / Biso min: 25.93 Å2
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Refinement step | Cycle: final / Resolution: 2.46→29.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.46→2.524 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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