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- PDB-1g3b: BOVINE BETA-TRYPSIN BOUND TO META-AMIDINO SCHIFF BASE MAGNESIUM(I... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1g3b | ||||||
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Title | BOVINE BETA-TRYPSIN BOUND TO META-AMIDINO SCHIFF BASE MAGNESIUM(II) CHELATE | ||||||
![]() | BETA-TRYPSIN | ||||||
![]() | HYDROLASE / enzyme-inhibitor complex / coordination metal based inhibitor | ||||||
Function / homology | ![]() trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Toyota, E. / Ng, K.K.S. / Sekizaki, H. / Itoh, K. / Tanizawa, K. / James, M.N.G. | ||||||
![]() | ![]() Title: X-ray crystallographic analyses of complexes between bovine beta-trypsin and Schiff base copper(II) or iron(III) chelates. Authors: Toyota, E. / Ng, K.K. / Sekizaki, H. / Itoh, K. / Tanizawa, K. / James, M.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.2 KB | Display | ![]() |
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PDB format | ![]() | 42 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.6 KB | Display | ![]() |
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Full document | ![]() | 451.7 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1g3cC ![]() 1g3dC ![]() 1g3eC ![]() 1btyS S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23913.820 Da / Num. of mol.: 1 / Fragment: MATURE ENZYME / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 174 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/108.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/108.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-108 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.91 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: magnesium sulfate, Tris-Cl, calcium chloride, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.15 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 106 K |
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Diffraction source | Source: ![]() |
Detector | Type: MACSCIENCE DIP100 / Detector: IMAGE PLATE / Date: Aug 19, 1999 / Details: mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: MONOCHROMATIC / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 26364 / Num. obs: 26364 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2540 / Rsym value: 0.353 / % possible all: 0.978 |
Reflection | *PLUS Lowest resolution: 25 Å |
Reflection shell | *PLUS % possible obs: 97.8 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1BTY Resolution: 1.8→19.35 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 233278.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.95 Å2 / ksol: 0.395 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.8 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.253 / % reflection Rfree: 9.5 % / Rfactor Rwork: 0.231 |