+Open data
-Basic information
Entry | Database: PDB / ID: 2tlx | ||||||
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Title | THERMOLYSIN (NATIVE) | ||||||
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 / SYNCHROTRON / ISOMORPHOUS REPLACEMENT / Resolution: 1.65 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. #1: Journal: Protein Sci. / Year: 1995 Title: Structural Analysis of Zinc Substitutions in the Active Site of Thermolysin Authors: Holland, D.R. / Hausrath, A.C. / Juers, D. / Matthews, B.W. #2: Journal: J.Mol.Biol. / Year: 1982 Title: Structure of Thermolysin Refined at 1.6 Angstrom Resolution Authors: Holmes, M.A. / Matthews, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2tlx.cif.gz | 83.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2tlx.ent.gz | 60.9 KB | Display | PDB format |
PDBx/mmJSON format | 2tlx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/2tlx ftp://data.pdbj.org/pub/pdb/validation_reports/tl/2tlx | HTTPS FTP |
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-Related structure data
Related structure data | 1tliC 1tlxC 2tliC 3tliC 4tliC 5tliC 6tliC 7tliC 8tliC 1lnfS C: citing same article (ref.) S: Starting model for refinement |
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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 , 6 types, 215 molecules
#2: Chemical | ChemComp-VAL / | ||||
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#3: Chemical | ChemComp-LYS / | ||||
#4: Chemical | ChemComp-ZN / | ||||
#5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-DMS / | #7: Water | ChemComp-HOH / | |
-Details
Compound details | THE ACTIVE SITE CLEFT OF THERMOLYSINonpolymer details | RESIDUES 317 AND 318 FORM A DIPEPTIDE (VAL-LYS) BOUND IN THE ACTIVE SITE OF THE MOLECULE. IT IS ...RESIDUES 317 AND 318 FORM A DIPEPTIDE (VAL-LYS) BOUND IN THE ACTIVE SITE OF THE MOLECULE. IT IS PRESUMED THAT THE ORIGIN OF THIS DIPEPTIDE IS THE C-TERMINAL TWO RESIDUES OF THE PROTEIN. SINCE THE C-TERMINUS APPEARS AT FULL OCCUPANCY, MOLECULES NOT INCORPORAT | |
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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: 49.42 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||
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: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Detector: CCD / Date: Jul 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. obs: 41876 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS REPLACEMENT Starting model: 1LNF Resolution: 1.65→20 Å / SU B: 1.5 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.08 Details: THIS ENTRY FORMS PART OF A SERIES OF STRUCTURES GENERATED FROM SOAKING CRYSTALS OF THERMOLYSIN IN ORGANIC SOLVENTS/ SOLUTES. THE CONDITIONS USED TO CRYSTALLIZE THERMOLYSIN WERE DIFFERENT TO ...Details: THIS ENTRY FORMS PART OF A SERIES OF STRUCTURES GENERATED FROM SOAKING CRYSTALS OF THERMOLYSIN IN ORGANIC SOLVENTS/ SOLUTES. THE CONDITIONS USED TO CRYSTALLIZE THERMOLYSIN WERE DIFFERENT TO THOSE OF HOLMES AND MATTHEWS (1982), HENCE IT WAS NECESSARY TO RE-REFINE THE NATIVE STRUCTURE.
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Displacement parameters | Biso mean: 19.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.188 / Rfactor Rwork: 0.163 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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