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Yorodumi- PDB-1bhc: BOVINE PANCREATIC TRYPSIN INHIBITOR CRYSTALLIZED FROM THIOCYANATE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bhc | ||||||
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Title | BOVINE PANCREATIC TRYPSIN INHIBITOR CRYSTALLIZED FROM THIOCYANATE | ||||||
Components | BOVINE PANCREATIC TRYPSIN INHIBITOR | ||||||
Keywords | PROTEASE INHIBITOR / TRYPSIN | ||||||
Function / homology | Function and homology information trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity / protease binding / calcium ion binding / extracellular space Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Hamiaux, C. / Prange, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: The decameric structure of bovine pancreatic trypsin inhibitor (BPTI) crystallized from thiocyanate at 2.7 A resolution. Authors: Hamiaux, C. / Prange, T. / Ries-Kautt, M. / Ducruix, A. / Lafont, S. / Astier, J.P. / Veesler, S. #1: Journal: J.Cryst.Growth / Year: 1997 Title: Comparison of Solubilities and Molecular Interactions of Bpti Molecules Giving Different Polymorphs Authors: Lafont, S. / Veesler, S. / Astier, J.P. / Boistelle, R. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Structure of Hexagonal Turkey Egg-White Lysozyme at 1.65 A Resolution Authors: Howell, P.L. #3: Journal: Acta Crystallogr.,Sect.B / Year: 1992 Title: Structure Determination of a Dimeric Form of Erabutoxin-B, Crystallized from a Thiocyanate Solution Authors: Saludjian, P. / Prange, T. / Navaza, J. / Menez, R. / Guilloteau, J.P. / Ries-Kautt, M. / Ducruix, A. #4: Journal: J.Mol.Biol. / Year: 1987 Title: Comparison of Two Highly Refined Structures of Bovine Pancreatic Trypsin Inhibitor Authors: Wlodawer, A. / Deisenhofer, J. / Huber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bhc.cif.gz | 118.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bhc.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bhc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bhc_validation.pdf.gz | 424.3 KB | Display | wwPDB validaton report |
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Full document | 1bhc_full_validation.pdf.gz | 436.2 KB | Display | |
Data in XML | 1bhc_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 1bhc_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/1bhc ftp://data.pdbj.org/pub/pdb/validation_reports/bh/1bhc | HTTPS FTP |
-Related structure data
Related structure data | 6ptiS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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-Components
#1: Protein | Mass: 6527.568 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00974 #2: Chemical | ChemComp-SCN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52 % |
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Crystal grow | pH: 4.5 Details: BPTI WAS CRYSTALLIZED FROM 250MM THIOCYANATE IN ACETATE BUFFER (50MM, PH=4.5) |
Crystal grow | *PLUS Method: other / Details: Lafont, S., (1997) J. Crystal Growth, 173, 132. |
-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→29.59 Å / Num. obs: 18308 / % possible obs: 85.5 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.63→2.71 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.186 / % possible all: 13.4 |
Reflection | *PLUS Num. measured all: 69959 |
Reflection shell | *PLUS % possible obs: 13.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 6PTI Resolution: 2.7→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: RESIDUES ARG1, ASP3, LYS15, LYS26 AND ARG39 APPEAR TO HAVE NCS BREAKDOWN IN RELATED MOLECULES. THEY WERE REMOVED FROM THE NCS RESTRAINT SCHEME. MET 52 WAS MODELLED WITH TWO CONFORMATIONS IN ...Details: RESIDUES ARG1, ASP3, LYS15, LYS26 AND ARG39 APPEAR TO HAVE NCS BREAKDOWN IN RELATED MOLECULES. THEY WERE REMOVED FROM THE NCS RESTRAINT SCHEME. MET 52 WAS MODELLED WITH TWO CONFORMATIONS IN ALL MOLECULES. 10 THIOCYANATE IONS AND 118 WATER MOLECULES ARE GIVEN FOLLOWING THE COORDINATES OF THE TEN MOLECULES. AS IN 6PTI, NO DENSITY WAS OBSERVED FOR THE TWO LAST RESIDUES (GLY 57 & ALA 58).
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Displacement parameters | Biso mean: 25.65 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.7→2.82 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.01 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.4 |