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Yorodumi- PDB-1zdp: Crystal Structure Analysis of Thermolysin Complexed with the Inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zdp | ||||||
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Title | Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (S)-thiorphan | ||||||
Components | Thermolysin | ||||||
Keywords | HYDROLASE / enzyme-inhibitor complex / zinc endopeptidase / gamma turn / thermostable | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Roderick, S.L. / Fournie-Zaluski, M.C. / Roques, B.P. / Matthews, B.W. | ||||||
Citation | Journal: Biochemistry / Year: 1989 Title: Thiorphan and retro-thiorphan display equivalent interactions when bound to crystalline thermolysin Authors: Roderick, S.L. / Fournie-Zaluski, M.C. / Roques, B.P. / 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 | 1zdp.cif.gz | 82.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zdp.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 1zdp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zdp_validation.pdf.gz | 770.3 KB | Display | wwPDB validaton report |
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Full document | 1zdp_full_validation.pdf.gz | 784.9 KB | Display | |
Data in XML | 1zdp_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 1zdp_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/1zdp ftp://data.pdbj.org/pub/pdb/validation_reports/zd/1zdp | HTTPS FTP |
-Related structure data
Related structure data | 1z9gC 3tln 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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Details | The enzyme acts as a monomer. |
-Components
#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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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-TIO / ( | #5: 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: 2.43 Å3/Da / Density % sol: 49 % |
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Crystal grow | Temperature: 277 K / Method: dilution with h2o / pH: 7.2 Details: Tris acetate, calcium acetate, DMSO, pH 7.20, dilution with H2O, temperature 277K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: KODAK / Detector: FILM / Date: 1987 / Details: GRAPHITE MONOCHROMATOR, COLLIMATING SLITS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 26142 / % possible obs: 68 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.038 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3TLN 3tln Resolution: 1.7→10 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: NONE / σ(F): 0 / Stereochemistry target values: TNT VERSION 1.0 / Details: 35 CYCLES OF CONJUGATE GRADIENT REFINEMENT
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Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refine LS restraints |
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