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Yorodumi- PDB-5j4q: alpha-chymotrypsin from bovine pancreas in complex with Bowman-Bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j4q | ||||||
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Title | alpha-chymotrypsin from bovine pancreas in complex with Bowman-Birk inhibitor from soybean | ||||||
Components |
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Keywords | HYDROLASE / protease inhibitor / protease | ||||||
Function / homology | Function and homology information 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 | Bos taurus (cattle) Glycine max (soybean) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.303 Å | ||||||
Authors | Johansson, E. / Tornoee, C.W. | ||||||
Citation | Journal: Synlett / Year: 2017 Title: Divergent Protein Synthesis of Bowman-Birk Protease Inhibitors, their Hydrodynamic Behavior and Co-crystallization with alpha-Chymotrypsin Authors: Tornoee, C.W. / Johansson, E. / Wahlund, P.-O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j4q.cif.gz | 71.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j4q.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 5j4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j4q_validation.pdf.gz | 438.7 KB | Display | wwPDB validaton report |
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Full document | 5j4q_full_validation.pdf.gz | 444.6 KB | Display | |
Data in XML | 5j4q_validation.xml.gz | 14 KB | Display | |
Data in CIF | 5j4q_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/5j4q ftp://data.pdbj.org/pub/pdb/validation_reports/j4/5j4q | HTTPS FTP |
-Related structure data
Related structure data | 5j4sC 1gl0S 1k9bS 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
#1: Protein | Mass: 25686.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Purchased from SIGMA-ALDRICH catalogue number C4129 Source: (natural) Bos taurus (cattle) / Organ: pancreas / References: UniProt: P00766, chymotrypsin |
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#2: Protein | Mass: 7880.859 Da / Num. of mol.: 1 / Fragment: UNP residues 40-110 / Source method: isolated from a natural source / Details: SIGMA-ALDRICH catalogue id T9777 / Source: (natural) Glycine max (soybean) / References: UniProt: P01055 |
#3: 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: 2.38 Å3/Da / Density % sol: 48.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 12%(w/v) PEG 20000, 0.1M MES, pH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.303→28.568 Å / Num. obs: 14141 / % possible obs: 98 % / Redundancy: 4.1 % / Biso Wilson estimate: 43.76 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.0987 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.303→2.386 Å / Redundancy: 4 % / Rmerge(I) obs: 0.7356 / Mean I/σ(I) obs: 1.82 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GL0,1K9B Resolution: 2.303→28.568 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.303→28.568 Å
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Refine LS restraints |
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LS refinement shell |
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