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Yorodumi- PDB-5fsp: Structure of thermolysin prepared by the 'soak-and-freeze' method... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fsp | ||||||
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Title | Structure of thermolysin prepared by the 'soak-and-freeze' method under 100 bar of krypton pressure | ||||||
Components | THERMOLYSIN | ||||||
Keywords | HYDROLASE / METALLOPROTEINASE / THERMOLYSINE / KRYPTON / PRESSURE / FLASH FREEZING | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Lafumat, B. / Mueller-Dieckmann, C. / Colloc'h, N. / Prange, T. / Royant, A. / van der Linden, p. / Carpentier, P. | ||||||
Citation | Journal: J.Appl.Crystallogr. / Year: 2016 Title: Gas-Sensitive Biological Crystals Processed in Pressurized Oxygen and Krypton Atmospheres: Deciphering Gas Channels in Proteins Using a Novel `Soak-and-Freeze' Methodology. Authors: Lafumat, B. / Mueller-Dieckmann, C. / Colloc'h, N. / Prange, T. / Royant, A. / van der Linden, P. / Carpentier, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fsp.cif.gz | 82.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fsp.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 5fsp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/5fsp ftp://data.pdbj.org/pub/pdb/validation_reports/fs/5fsp | HTTPS FTP |
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-Related structure data
Related structure data | 5frcC 5fsjC 5fssC 5fstC 3do1S 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 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 genetically manipulated source Source: (gene. exp.) BACILLUS THERMOPROTEOLYTICUS (bacteria) Production host: BACILLUS SUBTILIS (bacteria) / References: UniProt: P00800, thermolysin |
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-Non-polymers , 6 types, 300 molecules
#2: Chemical | ChemComp-VAL / | ||||
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#3: Chemical | ChemComp-LYS / | ||||
#4: Chemical | ChemComp-ZN / | ||||
#5: Chemical | ChemComp-KR / #6: Chemical | ChemComp-CA / #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: 2.3 Å3/Da / Density % sol: 45.79 % / Description: ANOMALOUS DATA |
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Crystal grow | pH: 6 Details: 1:1 WITH 50MM MES PH6, 1MNACL 45%(V/V) DMSO RESERVOIR: 35% SATURATED AMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.864 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.864 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 68932 / % possible obs: 99.7 % / Observed criterion σ(I): 5.8 / Redundancy: 17.4 % / Biso Wilson estimate: 12.49 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 16.7 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 5.82 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DO1 Resolution: 1.7→46.504 Å / SU ML: 0.14 / σ(F): 0.58 / Phase error: 16.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→46.504 Å
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Refine LS restraints |
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LS refinement shell |
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