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Yorodumi- PDB-2wbc: REFINED CRYSTAL STRUCTURE (2.3 ANGSTROM) OF A WINGED BEAN CHYMOTR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wbc | ||||||
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Title | REFINED CRYSTAL STRUCTURE (2.3 ANGSTROM) OF A WINGED BEAN CHYMOTRYPSIN INHIBITOR AND LOCATION OF ITS SECOND REACTIVE SITE | ||||||
Components | CHYMOTRYPSIN INHIBITOR | ||||||
Keywords | SERINE PROTEASE INHIBITOR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Psophocarpus tetragonolobus (winged bean) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Dattagupta, J.K. / Podder, A. / Chakrabarti, C. / Sen, U. / Mukhopadhyay, D. / Dutta, S.K. / Singh, M. | ||||||
Citation | Journal: Proteins / Year: 1999 Title: Refined crystal structure (2.3 A) of a double-headed winged bean alpha-chymotrypsin inhibitor and location of its second reactive site. Authors: Dattagupta, J.K. / Podder, A. / Chakrabarti, C. / Sen, U. / Mukhopadhyay, D. / Dutta, S.K. / Singh, M. #1: Journal: J.Mol.Biol. / Year: 1990 Title: Crystallization and Preliminary X-Ray Studies of Psophocarpin B1, a Chymotrypsin Inhibitor from Winged Bean Seeds Authors: Dattagupta, J.K. / Chakrabarti, C. / Podder, A. / Dutta, S.K. / Singh, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wbc.cif.gz | 56.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wbc.ent.gz | 46.2 KB | Display | PDB format |
PDBx/mmJSON format | 2wbc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/2wbc ftp://data.pdbj.org/pub/pdb/validation_reports/wb/2wbc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20266.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psophocarpus tetragonolobus (winged bean) / Tissue: SEED / References: UniProt: P10822 |
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#2: 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: 3.85 Å3/Da / Density % sol: 68 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: PROTEIN WAS CRYSTALLIZED BY HANGING DROP VAPOUR DIFFUSION FROM 25% AMM. SULPHATE IN TRIS-HCL, 10MM NA ACETATE,400 MM NACL AT PH 5.4 AGAINST 25% AMM. SULPHATE,60MM NA ACETATE AT 4 DEGREE ...Details: PROTEIN WAS CRYSTALLIZED BY HANGING DROP VAPOUR DIFFUSION FROM 25% AMM. SULPHATE IN TRIS-HCL, 10MM NA ACETATE,400 MM NACL AT PH 5.4 AGAINST 25% AMM. SULPHATE,60MM NA ACETATE AT 4 DEGREE CENTIGRADE., vapor diffusion - hanging drop, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→12 Å / Num. obs: 9897 / % possible obs: 80.1 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.095 |
Reflection | *PLUS Num. measured all: 10551 |
-Processing
Software |
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Refinement | Resolution: 2.3→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: THE ELECTRON DENSITY IS CONTINUOUS FOR ALL THE MAIN CHAIN ATOMS. HOWEVER THE FITTING OF THE MODEL TO THE ELECTRON DENSITY MAP IN THE RESIDUE RANGES 137 - 142, AND 176 - 183 IS SOMEWHAT POOR. ...Details: THE ELECTRON DENSITY IS CONTINUOUS FOR ALL THE MAIN CHAIN ATOMS. HOWEVER THE FITTING OF THE MODEL TO THE ELECTRON DENSITY MAP IN THE RESIDUE RANGES 137 - 142, AND 176 - 183 IS SOMEWHAT POOR. WCI HAS BEEN FOUND TO BE SPHERICAL AND CONSISTS OF 12 ANTIPARALLEL BETA-STRANDS WITH CONNECTING LOOPS ARRANGED IN A CHARACTERISTIC B-TREFOIL TYPE FOLDING. A PSEUDO THREE-FOLD AXIS EXISTS PARALLEL TO THE BARREL AXIS OF THE STRUCTURE. EACH OF THE THREE SUBDOMAINS COMPRISES FOUR B-STRANDS WITH CONNECTING LOOPS. FROM THIS HIGHER RESOLUTION MODEL THE LOCATION OF THE SECOND REACTIVE SITE OF THE INHIBITOR PROTEIN COULD BE IDENTIFIED MAINLY ON THE BASIS OF STRUCTURAL STUDIES.
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Displacement parameters | Biso mean: 30.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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