+Open data
-Basic information
Entry | Database: PDB / ID: 2tli | ||||||
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Title | THERMOLYSIN (5% ISOPROPANOL SOAKED CRYSTALS) | ||||||
Components | THERMOLYSIN | ||||||
Keywords | HYDROLASE / METALLOPROTEINASE / ORGANIC SOLVENT | ||||||
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 / ISOMORPHOUS REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | English, A.C. / Done, S.H. / Groom, C.R. / Hubbard, R.E. | ||||||
Citation | Journal: Proteins / Year: 1999 Title: Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol. Authors: English, A.C. / Done, S.H. / Caves, L.S. / Groom, C.R. / Hubbard, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2tli.cif.gz | 79.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2tli.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 2tli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2tli_validation.pdf.gz | 448.6 KB | Display | wwPDB validaton report |
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Full document | 2tli_full_validation.pdf.gz | 453 KB | Display | |
Data in XML | 2tli_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 2tli_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/2tli ftp://data.pdbj.org/pub/pdb/validation_reports/tl/2tli | HTTPS FTP |
-Related structure data
Related structure data | 1tliC 1tlxC 2tlxC 3tliC 4tliC 5tliC 6tliC 7tliC 8tliC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34362.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin |
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-Non-polymers , 5 types, 160 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-IPA / | #6: Water | ChemComp-HOH / | |
-Details
Compound details | THE ACTIVE SITE CLEFT OF THERMOLYSI |
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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: 2.43 Å3/Da / Density % sol: 49.33 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1997 |
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→30 Å / Num. obs: 23955 / % possible obs: 95 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.95→2.08 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 3.2 / % possible all: 92 |
Reflection shell | *PLUS % possible obs: 92 % |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS REPLACEMENT / Resolution: 1.95→30 Å / SU B: 2.81 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.15 Details: THIS ENTRY FORMS PART OF A SERIES OF STRUCTURES GENERATED FROM SOAKING CRYSTALS OF THERMOLYSIN IN ISOPROPANOL. AT THIS CONCENTRATION (5% ISOPROPANOL) A SINGLE MOLECULE OF ISOPROPANOL IS ...Details: THIS ENTRY FORMS PART OF A SERIES OF STRUCTURES GENERATED FROM SOAKING CRYSTALS OF THERMOLYSIN IN ISOPROPANOL. AT THIS CONCENTRATION (5% ISOPROPANOL) A SINGLE MOLECULE OF ISOPROPANOL IS BOUND IN THE S1(PRIME) SUBSITE.
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Displacement parameters | Biso mean: 26.9 Å2 / Baniso 23: 0 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→30 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.219 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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