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- PDB-3mnx: Investigation of global and local effects of radiation damage on ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mnx | ||||||
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Title | Investigation of global and local effects of radiation damage on porcine pancreatic elastase. Fourth stage of radiation damage | ||||||
![]() | Chymotrypsin-like elastase family member 1 | ||||||
![]() | HYDROLASE / radiation damage / disulfide bridge / atomic resolution | ||||||
Function / homology | ![]() pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Petrova, T. / Ginell, S. / Kim, Y. / Joachimiak, G. / Joachimiak, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.6 KB | Display | ![]() |
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PDB format | ![]() | 107.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3mnbC ![]() 3mncC ![]() 3mnsC ![]() 3mo3C ![]() 3mo6C ![]() 3mo9C ![]() 3mocC ![]() 3mtyC ![]() 3mu0C ![]() 3mu1C ![]() 3mu4C ![]() 3mu5C ![]() 3mu8C ![]() 3oddC ![]() 3odfC ![]() 1gvkS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() | ||
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#2: Chemical | ChemComp-NA / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.27 % |
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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, 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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.4→50 Å / Num. obs: 43146 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 25.88 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 2.27 / Num. unique all: 2141 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GVK Resolution: 1.386→9.835 Å / SU ML: 0.13 / Isotropic thermal model: Anisotropic / σ(F): 0.05 / Phase error: 12.07 / 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: 78.348 Å2 / ksol: 0.341 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.24 Å2
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Refine analyze | Luzzati coordinate error obs: 0.13 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.386→9.835 Å
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Refine LS restraints |
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LS refinement shell |
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