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Yorodumi- PDB-1g6x: ULTRA HIGH RESOLUTION STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHI... -
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-Basic information
Entry | Database: PDB / ID: 1g6x | ||||||
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Title | ULTRA HIGH RESOLUTION STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHIBITOR (BPTI) MUTANT WITH ALTERED BINDING LOOP SEQUENCE | ||||||
Components | PANCREATIC TRYPSIN INHIBITOR | ||||||
Keywords | HYDROLASE INHIBITOR / SERINE PROTEASE INHIBITOR | ||||||
Function / homology | Function and homology information trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / serine protease inhibitor complex / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine-type endopeptidase inhibitor activity ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / serine protease inhibitor complex / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / 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 / EXISTING MODEL / Resolution: 0.86 Å | ||||||
Authors | Addlagatta, A. / Czapinska, H. / Krzywda, S. / Otlewski, J. / Jaskolski, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Ultrahigh-resolution structure of a BPTI mutant. Authors: Addlagatta, A. / Krzywda, S. / Czapinska, H. / Otlewski, J. / Jaskolski, M. #1: Journal: J.Mol.Biol. / Year: 2000 Title: High-Resolution Structure of Bovine Pancreatic Trypsin Inhibitor with Altered Binding Loop Sequenc Authors: Czapinska, H. / Otlewski, J. / Krzywda, S. / Sheldrick, G.M. / Jaskolski, M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Structure of Bovine Pancreatic Trypsin Inhibitor at 125 K: Definition of Carboxyl-Terminal Residues Gly57 and Ala58 Authors: Parkin, S. / Rupp, B. / Hope, H. #3: Journal: J.Mol.Biol. / Year: 1992 Title: Determination of a High Quality Nuclear Magnetic Resonance Solution Structure of the Bovine Pancreatic Trypsin Inhibitor and Comparison with Three Crystal Structures Authors: Berndt, K. / Guentert, P. / Orbons, L.P. / Wuethrich, K. #4: Journal: J.Mol.Biol. / Year: 1984 Title: Structure of Bovine Pancreatic Trypsin Inhibitor . Results of Joint Neutron and X-Ray Refinement of Crystal Form II Authors: Wlodawer, A. / Walter, J. / Huber, R. / Sjolin, L. #5: Journal: Acta Crystallogr.,Sect.B / Year: 1975 Title: Crystallographic Refinement of the Structure of Bovine Pancreatic Trypsin Inhibitor at 1.5 A Resolution Authors: Deisenhofer, J. / Steigemann, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g6x.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g6x.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 1g6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g6x_validation.pdf.gz | 432.8 KB | Display | wwPDB validaton report |
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Full document | 1g6x_full_validation.pdf.gz | 437 KB | Display | |
Data in XML | 1g6x_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1g6x_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/1g6x ftp://data.pdbj.org/pub/pdb/validation_reports/g6/1g6x | HTTPS FTP |
-Related structure data
Related structure data | 1qlqS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 6481.481 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P00974 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 2.28 Å3/Da / Density % sol: 46 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2% PEG 400, 2 M AMMONIUM SULFATE, 0.1 M NA HEPES. A PROTEIN SAMPLE, LYOPHILIZED AFTER HPLC PURIFICATION FROM TFA/ACETONITRILE MIXTURE, WAS DISSOLVED IN WATER TO A CONCENTRATION OF 9 MG/2 UL ...Details: 2% PEG 400, 2 M AMMONIUM SULFATE, 0.1 M NA HEPES. A PROTEIN SAMPLE, LYOPHILIZED AFTER HPLC PURIFICATION FROM TFA/ACETONITRILE MIXTURE, WAS DISSOLVED IN WATER TO A CONCENTRATION OF 9 MG/2 UL DROPS OF THE PROTEIN SOLUTION WERE MIXED WITH 2 UL OF RESERVOIR SOLUTION CONTAINING 2% PEG 400, 2 M AMMONIUM SULFATE AND 0.1 M NA HEPES, PH 7.5. THE HANGING DROPLETS WERE EQUILIBRATED AT 19 DEG C THROUGH THE GAS PHASE WITH THE RESERVOIR. PRISMATIC CRYSTALS MEASURING UP TO 0.4 MM GREW WITHIN 12 HOURS. FOR LOW-TEMPERATURE DATA COLLECTION (100 K), THE CRYSTAL WAS CRYOPROTECTED IN THE RESERVOIR SOLUTION SUPPLEMENTED BY 30 % ETHYLENE GLYCOL., VAPOR DIFFUSION, HANGING DROP, temperature 292K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / pH: 7 / Details: Czapinska, H., (2000) J.Mol.Biol., 295, 1237. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.909 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 7, 1999 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.909 Å / Relative weight: 1 |
Reflection | Resolution: 0.86→20 Å / Num. obs: 47018 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 17.3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 54.1 |
Reflection shell | Resolution: 0.86→0.9 Å / Redundancy: 6 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3.61 / % possible all: 88.6 |
Reflection | *PLUS Num. measured all: 814213 |
Reflection shell | *PLUS % possible obs: 88.6 % |
-Processing
Software |
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Refinement | Method to determine structure: EXISTING MODEL Starting model: 1QLQ Resolution: 0.86→10 Å / Num. parameters: 6499 / Num. restraintsaints: 7361 / Cross valid method: FREE R StereochEM target val spec case: ETHYLENE GLYCOL (EDO) AND SULFATE (SO4) GEOMETRY BASED ON DATA FROM CSD Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT WITHOUT STEREOCHEMICAL RESTRAINTS ON ORDERED MAIN CHAIN. THE COMPLETE C-TERMINUS IS VISIBLE. IT FORMS A SALT-BRIDGE WITH THE N-TERMINUS. ARG 39 IS DISORDERED IN TWO ...Details: ANISOTROPIC REFINEMENT WITHOUT STEREOCHEMICAL RESTRAINTS ON ORDERED MAIN CHAIN. THE COMPLETE C-TERMINUS IS VISIBLE. IT FORMS A SALT-BRIDGE WITH THE N-TERMINUS. ARG 39 IS DISORDERED IN TWO CONFORMATIONS. IN ADDITION, IT IS ADJACENT TO CYS 38 OF THE DISORDERED 14-38 DISULFIDE AND IS PART OF A DISORDERED ARGININE CAGE. ALA 58 IS THE C-TERMINAL RESIDUE. IT IMMEDIATELY FOLLOWS THE DISORDERED GLY 56 - GLY 57 DOUBLET. THE CYS14-CYS38 DISULFIDE BRIDGE IS OBSERVED IN TWO DISTINCT CHIRALITIES (60 % RIGHT-HANDED, 40 % LEFT-HANDED). THE MAIN CHAIN OF THREE RESIDUES AND THE SIDE CHAINS OF 10 RESIDUES ARE MODELED IN TWO CONFORMATIONS. EIGHT SULFATE ANIONS (TWO WITH TWO-FOLD SYMMETRY) ARE PRESENT IN THE ASYMMETRIC UNIT. ONE OF THEM SHARES A SITE WITH THREE WATER MOLECULES. TWO ETHYLENE GLYCOL MOLECULES MODELED PER ONE PROTEIN MOLECULE. REFINEMENT CONCLUDED USING ONE CYCLE OF BLOCKED FULL-MATRIX LEAST-SQUARES ALGORITHM.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 12 / Occupancy sum hydrogen: 426 / Occupancy sum non hydrogen: 603 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.86→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 4 % / Rfactor Rfree: 0.14 / Rfactor Rwork: 0.107 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_chiral_restr / Dev ideal: 0.113 |