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Open data
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Basic information
Entry | Database: PDB / ID: 4oi5 | ||||||
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Title | Glycerol-free structure of thermolysin in complex with ubtln58 | ||||||
![]() | Thermolysin | ||||||
![]() | Hydrolase/Hydrolase Inhibitor / Protease / Metalloprotease / Hydrolysis / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | ![]() thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Krimmer, S.G. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: Methyl, Ethyl, Propyl, Butyl: Futile But Not for Water, as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors. Authors: Krimmer, S.G. / Betz, M. / Heine, A. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.9 KB | Display | ![]() |
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PDB format | ![]() | 127.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 707.4 KB | Display | ![]() |
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Full document | ![]() | 707.4 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 28.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mtwC ![]() 4mwpC ![]() 4mxjC ![]() 4mznC ![]() 4n4eC ![]() 4n5pC ![]() 4n66C ![]() 8tlnS 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules E
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 / Fragment: UNP residues 233-548 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 465 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/2G6.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/2G6.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-2G6 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 50 mM Tris/HCl, 1.9 M CsCl, 50% DMSO, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 18, 2013 / Details: Mirror |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 80778 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 8.946 Å2 / Rsym value: 0.079 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3.72 / Num. unique all: 3965 / Rsym value: 0.487 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8TLN Resolution: 1.3→19.649 Å / SU ML: 0.09 / Cross valid method: R-free / σ(F): 1.35 / Phase error: 12.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→19.649 Å
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Refine LS restraints |
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LS refinement shell |
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