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Yorodumi- PDB-3bg4: The crystal structure of guamerin in complex with chymotrypsin an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bg4 | ||||||
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Title | The crystal structure of guamerin in complex with chymotrypsin and the development of an elastase-specific inhibitor | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / guamerin / chymotrypsin / elastase / inhibitor / Digestion / Hydrolase / Protease / Secreted / Serine protease / Zymogen / Protease inhibitor / Serine protease inhibitor / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of coagulation / chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Hirudo nipponia (invertebrata) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kim, H. / Chu, T.T.T. / Kim, D.Y. / Kim, D.R. / Nguyen, C.M.T. / Choi, J. / Lee, J.R. / Hahn, M.J. / Kim, K.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: The crystal structure of guamerin in complex with chymotrypsin and the development of an elastase-specific inhibitor. Authors: Kim, H. / Chu, T.T.T. / Kim, D.Y. / Kim, D.R. / Nguyen, C.M.T. / Choi, J. / Lee, J.R. / Hahn, M.J. / Kim, K.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bg4.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bg4.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 3bg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/3bg4 ftp://data.pdbj.org/pub/pdb/validation_reports/bg/3bg4 | HTTPS FTP |
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-Related structure data
Related structure data | 1choS S: Starting model for refinement |
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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
#1: Protein/peptide | Mass: 1253.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P00766, UniProt: P00767*PLUS, chymotrypsin |
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#2: Protein | Mass: 13934.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin |
#3: Protein | Mass: 10074.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin |
#4: Protein | Mass: 6126.907 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hirudo nipponia (invertebrata) / Production host: Pichia pastoris (fungus) / References: UniProt: P46443 |
#5: 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: 1.9 Å3/Da / Density % sol: 35.31 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris-HCl, 0.2M MgCl2, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 27, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 8762 / Num. obs: 7343 / % possible obs: 83.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 30.5 Å2 / Rsym value: 0.114 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 876 / Rsym value: 0.256 / % possible all: 82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CHO Resolution: 2.5→29.94 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1261500.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.8757 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 10
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Xplor file |
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