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- PDB-5r46: Crystal Structure of deuterated gamma-Chymotrypsin at pH 5.6, roo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5r46 | |||||||||
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Title | Crystal Structure of deuterated gamma-Chymotrypsin at pH 5.6, room temperature | |||||||||
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![]() | HYDROLASE / serine protease / hydrolase-peptide complex | |||||||||
Function / homology | ![]() chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kreinbring, C.A. / Wilson, M.A. / Kovalevsky, A.Y. / Blakeley, M.P. / Fisher, S.Z. / Lazar, L.M. / Moulin, A.G. / Novak, W.R. / Petsko, G.A. / Ringe, D. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Effect of Temperature and pH on Ionizable Residues in gamma-Chymotrypsin: a X-ray and Neutron Crystallography Study Authors: Kreinbring, C.A. / Wilson, M.A. / Kovalevsky, A.Y. / Blakeley, M.P. / Fisher, S.Z. / Lazar, L.M. / Moulin, A.G. / Novak, W.R. / Petsko, G.A. / Ringe, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.5 KB | Display | ![]() |
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PDB format | ![]() | 91.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.1 KB | Display | ![]() |
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Full document | ![]() | 465.1 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Group deposition
ID | G_1002095 (4 entries) |
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Title | Effect of Temperature and pH on Ionizable Residues in gamma-Chymotrypsin: a X-ray and Neutron Crystallography Study |
Type | undefined |
Description | gamma-Chymotrypsin at pH 5.6 |
-Related structure data
Related structure data | ![]() 1gctS 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 on special symmetry positions |
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Components
-Protein/peptide , 3 types, 3 molecules ADE
#1: Protein/peptide | Mass: 1253.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#4: Protein/peptide | Mass: 574.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein/peptide | Mass: 535.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 2 types, 2 molecules BC
#2: Protein | Mass: 13934.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#3: Protein | Mass: 10074.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 3 types, 168 molecules ![](data/chem/img/IOD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-IOD / | ||
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#7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.02 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop Details: 45% saturated ammonium sulfate, 0.75% saturated cetyltrimethylammonium bromide, 100 mM sodium iodide; sodium malonate PH range: 10 mM sodium cacodylate pH 6.0 |
-Data collection
Diffraction | Mean temperature: 297 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.05→50 Å / Num. obs: 111717 / % possible obs: 99.6 % / Redundancy: 39.3 % / Rmerge(I) obs: 0.109 / Χ2: 1.125 / Net I/σ(I): 13.1 / Num. measured all: 4389000 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GCT Resolution: 1.05→56.64 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.484 / SU ML: 0.011 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.019 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.66 Å2 / Biso mean: 17.772 Å2 / Biso min: 8.97 Å2
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Refinement step | Cycle: final / Resolution: 1.05→56.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.05→1.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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