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Yorodumi- PDB-3mnb: Investigation of global and local effects of radiation damage on ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mnb | ||||||
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Title | Investigation of global and local effects of radiation damage on porcine pancreatic elastase. First stage 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: 1.198 Å | ||||||
Authors | Petrova, T. / Ginell, S. / Kim, Y. / Joachimiak, G. / 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 | 3mnb.cif.gz | 137.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mnb.ent.gz | 105.5 KB | Display | PDB format |
PDBx/mmJSON format | 3mnb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/3mnb ftp://data.pdbj.org/pub/pdb/validation_reports/mn/3mnb | HTTPS FTP |
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-Related structure data
Related structure data | 3mncC 3mnsC 3mnxC 3mo3C 3mo6C 3mo9C 3mocC 3mtyC 3mu0C 3mu1C 3mu4C 3mu5C 3mu8C 3oddC 3odfC 1gvkS 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: 40.51 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: The initial concentration of the protein was 10 mg/ml in water. The reservoir contained 25 mM Na2SO4. The cryo-solution contained 25 mM Na2SO4 and 25% glycerol, pH 8.2, VAPOR DIFFUSION, ...Details: The initial concentration of the protein was 10 mg/ml in water. The reservoir contained 25 mM Na2SO4. The cryo-solution contained 25 mM Na2SO4 and 25% glycerol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 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: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. all: 68113 / Num. obs: 68040 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 9.89 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 33.7 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 5 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3340 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GVK Resolution: 1.198→45.575 Å / Isotropic thermal model: Anisotropic / σ(I): 0.14 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 15.8 Å2
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Refine analyze | Luzzati coordinate error obs: 0.09 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.198→45.575 Å
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Refine LS restraints |
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LS refinement shell |
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