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Yorodumi- PDB-6yms: Structural and Kinetic Evaluation of Phosphoramidate Inhibitors o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yms | ||||||
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Title | Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin | ||||||
Components | Thermolysin | ||||||
Keywords | HYDROLASE / Phosphoramidate Inhibitor / Protease | ||||||
Function / homology | Function and homology information thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | ||||||
Authors | Kljajic, M. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To Be Published Title: Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin Authors: Kljajic, M. / Gerber, H.-D. / Heine, A. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yms.cif.gz | 249 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yms.ent.gz | 167.6 KB | Display | PDB format |
PDBx/mmJSON format | 6yms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yms_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6yms_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6yms_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 6yms_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/6yms ftp://data.pdbj.org/pub/pdb/validation_reports/ym/6yms | HTTPS FTP |
-Related structure data
Related structure data | 6y4iC 6yi6C 6ymrC 5lvdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: nprS, nprM / Production host: Geobacillus stearothermophilus (bacteria) / References: UniProt: P43133, thermolysin |
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-Non-polymers , 7 types, 373 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / | #4: Chemical | #5: Chemical | ChemComp-OZH / ( | #6: Chemical | ChemComp-TRS / | #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.49 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.0 M CsCl, 50 mM Tris(hydroxymethyl)aminomethane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→46.31 Å / Num. obs: 76712 / % possible obs: 98.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 16.91 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.083 / Rsym value: 0.08 / Net I/σ(I): 19.89 |
Reflection shell | Resolution: 1.32→1.4 Å / Mean I/σ(I) obs: 4.55 / Num. unique obs: 12067 / CC1/2: 0.94 / Rrim(I) all: 0.516 / Rsym value: 0.495 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LVD Resolution: 1.32→46.31 Å / SU ML: 0.0813 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.3655
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.32→46.31 Å
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Refine LS restraints |
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LS refinement shell |
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