+Open data
-Basic information
Entry | Database: PDB / ID: 1fjt | ||||||
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Title | THERMOLYSIN (50% ACETONITRILE 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: 2.2 Å | ||||||
Authors | English, A.C. / Groom, C.R. / Hubbard, R.E. | ||||||
Citation | Journal: Protein Eng. / Year: 2001 Title: Experimental and computational mapping of the binding surface of a crystalline protein. Authors: English, A.C. / 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 | 1fjt.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fjt.ent.gz | 59.8 KB | Display | PDB format |
PDBx/mmJSON format | 1fjt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fjt_validation.pdf.gz | 404 KB | Display | wwPDB validaton report |
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Full document | 1fjt_full_validation.pdf.gz | 409.6 KB | Display | |
Data in XML | 1fjt_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 1fjt_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/1fjt ftp://data.pdbj.org/pub/pdb/validation_reports/fj/1fjt | HTTPS FTP |
-Related structure data
Related structure data | 1fj3C 1fjoC 1fjqC 1fjuC 1fjvC 1fjwC 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 , 6 types, 167 molecules
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-VAL / | #6: Chemical | ChemComp-LYS / | #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: 2.42 Å3/Da / Density % sol: 49.23 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 4.6MM THERMOLYSIN, 45% DMSO, 50MM TRIS-HCL, 2.5M CSCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknownDetails: English, A.C., (1999) Proteins Struct.Funct.Genet., 37, 628. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Nov 6, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 161170 / Num. obs: 19030 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.38 / Num. unique all: 22857 / % possible all: 91 |
Reflection | *PLUS % possible obs: 93 % |
Reflection shell | *PLUS % possible obs: 91 % / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: isomorphous replacement / Resolution: 2.2→20 Å / σ(I): 2 / Stereochemistry target values: Engh & Huber Details: Maximim likelihood procedure used AT THIS CONCENTRATION (50% ACETONITRILE) THERE IS ELECTRON DENSITY CORRESPONDING TO THE DIPEPTIDE (VAL506-LYS507) OBSERVED IN THE ACTIVE SITE OF THE NATIVE ENZYME.
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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