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Yorodumi- PDB-6d5s: Hexagonal thermolysin cryocooled to 100 K with 50% MPD as cryopro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d5s | ||||||
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Title | Hexagonal thermolysin cryocooled to 100 K with 50% MPD as cryoprotectant | ||||||
Components | Thermolysin | ||||||
Keywords | HYDROLASE / zinc protease | ||||||
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: 2.00003547199 Å | ||||||
Authors | Juers, D.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order. Authors: Juers, D.H. / Farley, C.A. / Saxby, C.P. / Cotter, R.A. / Cahn, J.K.B. / Holton-Burke, R.C. / Harrison, K. / Wu, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d5s.cif.gz | 169 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d5s.ent.gz | 109 KB | Display | PDB format |
PDBx/mmJSON format | 6d5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/6d5s ftp://data.pdbj.org/pub/pdb/validation_reports/d5/6d5s | HTTPS FTP |
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-Related structure data
Related structure data | 5un3C 5uu7C 5uu8C 5uu9C 5uuaC 5uubC 5uucC 5uudC 5uueC 6avlC 6b6nC 6b6oC 6b6pC 6b6qC 6b6rC 6b6sC 6b6tC 6d5nC 6d5oC 6d5pC 6d5qC 6d5rC 6d5tC 6d5uC 6d6eC 6d6fC 6d6gC 6d6hC 6dzfC 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 natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin |
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-Non-polymers , 6 types, 314 molecules
#2: Chemical | ChemComp-VAL / | ||||
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#3: Chemical | ChemComp-LYS / | ||||
#4: Chemical | ChemComp-ZN / | ||||
#5: Chemical | ChemComp-CA / #6: Chemical | #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: 2.32 Å3/Da / Density % sol: 47.02 % / Description: Hexagonal prism |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: Protein: 100 mg/mL in 45% dams Well: 2 M AmSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: Agilent SuperNova / Wavelength: 1.54 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Jul 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→13.81 Å / Num. obs: 22529 / % possible obs: 98.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 12.922627996 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.12 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2→2.1 Å / Mean I/σ(I) obs: 4.4 / CC1/2: 0.903 / Rrim(I) all: 0.425 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.00003547199→13.8084334859 Å / SU ML: 0.171264351156 / Cross valid method: FREE R-VALUE / σ(F): 1.34352743297 / Phase error: 17.529397584
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.2645845833 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.00003547199→13.8084334859 Å
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Refine LS restraints |
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LS refinement shell |
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