+Open data
-Basic information
Entry | Database: PDB / ID: 2wi0 | ||||||
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Title | Dipeptide Inhibitors of Thermolysin | ||||||
Components | THERMOLYSIN | ||||||
Keywords | HYDROLASE / METAL-BINDING | ||||||
Function / homology | Function and homology information thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | BACILLUS THERMOPROTEOLYTICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Lund, B.A. / Leiros, I. / Leiros, H.-K.S. | ||||||
Citation | Journal: To be Published Title: Dipeptide Inhibitors of Thermolysin Authors: Lund, B.A. / Leiros, I. / Leiros, H.-K.S. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wi0.cif.gz | 87.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wi0.ent.gz | 65.6 KB | Display | PDB format |
PDBx/mmJSON format | 2wi0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/2wi0 ftp://data.pdbj.org/pub/pdb/validation_reports/wi/2wi0 | HTTPS FTP |
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-Related structure data
Related structure data | 2whzC 2tlxS 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 A
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THE DI-PEPTIDE LW IS BOUND TO THE PROTEIN Source: (gene. exp.) BACILLUS THERMOPROTEOLYTICUS (bacteria) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00800, thermolysin |
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-Non-polymers , 6 types, 335 molecules
#2: Chemical | ChemComp-LEU / | ||||
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#3: Chemical | ChemComp-TRP / | ||||
#4: Chemical | ChemComp-ZN / | ||||
#5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 37.55 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. obs: 23837 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 19.33 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.2 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2TLX Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.489 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 mean: 18.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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