[English] 日本語
Yorodumi- PDB-3mns: Investigation of global and local effects of radiation damage on ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mns | ||||||
---|---|---|---|---|---|---|---|
Title | Investigation of global and local effects of radiation damage on porcine pancreatic elastase. Third 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: 1.497 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3mns.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3mns.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 3mns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/3mns ftp://data.pdbj.org/pub/pdb/validation_reports/mn/3mns | HTTPS FTP |
---|
-Related structure data
Related structure data | 3mnbC 3mncC 3mnxC 3mo3C 3mo6C 3mo9C 3mocC 3mtyC 3mu0C 3mu1C 3mu4C 3mu5C 3mu8C 3oddC 3odfC 1gvkS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 | ||
---|---|---|---|
#2: Chemical | ChemComp-NA / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.97 % |
---|---|
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, pH = 8.2. The cryo-solution contained 25 mM Na2SO4 and 25% glycerol, VAPOR DIFFUSION, ...Details: The initial concentration of the protein was 10 mg/ml in water. The reservoir contained 25 mM Na2SO4, pH = 8.2. The cryo-solution contained 25 mM Na2SO4 and 25% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 1.5→50 Å / Num. obs: 35266 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 14.37 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 33.4 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 2.64 / Num. unique all: 1753 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GVK Resolution: 1.497→45.668 Å / SU ML: 0.16 / Isotropic thermal model: Isotropic / σ(F): 0.11 / Phase error: 14.78 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 97.427 Å2 / ksol: 0.389 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.68 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.16 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.497→45.668 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|