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Yorodumi- PDB-3mu1: Comparison of the character and the speed of X-ray-induced struct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mu1 | ||||||
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Title | Comparison of the character and the speed of X-ray-induced structural changes of porcine pancreatic elastase at two temperatures, 100 and 15K. The data set was collected from region A of the crystal. Fifth step of radiation damage | ||||||
Components | Chymotrypsin-like elastase family member 1 | ||||||
Keywords | HYDROLASE / radiation damage / disulfide bridge / atomic resolution | ||||||
Function / homology | Function and homology information pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Petrova, T. / Ginell, S. / Mitschler, A. / Cousido-Siah, A. / Hazemann, I. / Podjarny, A. / Joachimiak, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: X-ray-induced deterioration of disulfide bridges at atomic resolution. Authors: Petrova, T. / Ginell, S. / Mitschler, A. / Kim, Y. / Lunin, V.Y. / Joachimiak, G. / Cousido-Siah, A. / Hazemann, I. / Podjarny, A. / Lazarski, K. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mu1.cif.gz | 77.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mu1.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 3mu1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/3mu1 ftp://data.pdbj.org/pub/pdb/validation_reports/mu/3mu1 | HTTPS FTP |
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-Related structure data
Related structure data | 3mnbC 3mncC 3mnsC 3mnxC 3mo3C 3mo6C 3mo9C 3mocC 3mtyC 3mu0C 3mu4C 3mu5C 3mu8C 3oddC 3odfC 1gvkS 3mt4 S: Starting model for refinement 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
#1: Protein | Mass: 25928.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase | ||
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#2: Chemical | ChemComp-NA / | ||
#3: Chemical | #4: 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: 2.07 Å3/Da / Density % sol: 40.71 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: The initial concentration of the protein was 20 mg/ml in 10% glycerol solution. The reservoir contained a 250 mM Na2SO4. For cryo-protection, it was supplemented with 25% glycerol, pH 7.5, ...Details: The initial concentration of the protein was 20 mg/ml in 10% glycerol solution. The reservoir contained a 250 mM Na2SO4. For cryo-protection, it was supplemented with 25% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97895 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2008 Details: 1.02-M FLAT MIRROR MADE OF ZERODUR PROVIDING VERTICAL FOCUSING AND REJECTION OF HARMONIC CONTAMINATION |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR UTILIZING A SI-111 AND SAGITAL HORIZONTAL FOCUSING Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97895 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→50 Å / Num. obs: 22233 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 20.22 Å2 / Rmerge(I) obs: 0.027 / Net I/σ(I): 30.52 |
Reflection shell | Resolution: 1.74→1.81 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 3.54 / Num. unique all: 2190 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1GVK Resolution: 1.74→18.773 Å / SU ML: 0.23 / Isotropic thermal model: Isotropic / σ(F): 0.17 / 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 / Bsol: 126.469 Å2 / ksol: 0.402 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.02 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→18.773 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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