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Yorodumi- PDB-1g3b: BOVINE BETA-TRYPSIN BOUND TO META-AMIDINO SCHIFF BASE MAGNESIUM(I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g3b | ||||||
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Title | BOVINE BETA-TRYPSIN BOUND TO META-AMIDINO SCHIFF BASE MAGNESIUM(II) CHELATE | ||||||
Components | BETA-TRYPSIN | ||||||
Keywords | HYDROLASE / enzyme-inhibitor complex / coordination metal based inhibitor | ||||||
Function / homology | Function and homology information cap snatching / virion component / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Toyota, E. / Ng, K.K.S. / Sekizaki, H. / Itoh, K. / Tanizawa, K. / James, M.N.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g3b.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g3b.ent.gz | 42 KB | Display | PDB format |
PDBx/mmJSON format | 1g3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g3b_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
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Full document | 1g3b_full_validation.pdf.gz | 451.7 KB | Display | |
Data in XML | 1g3b_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 1g3b_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/1g3b ftp://data.pdbj.org/pub/pdb/validation_reports/g3/1g3b | HTTPS FTP |
-Related structure data
Related structure data | 1g3cC 1g3dC 1g3eC 1btyS 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
-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) Bos taurus (cattle) / Secretion: PANCREAS / References: UniProt: P00760, trypsin |
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-Non-polymers , 5 types, 174 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS 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 |