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Yorodumi- PDB-7a0d: The Crystal Structure of Bovine Thrombin in complex with Hirudin ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a0d | ||||||
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Title | The Crystal Structure of Bovine Thrombin in complex with Hirudin (C16U/C28U) at 1.6 Angstroms Resolution | ||||||
Components |
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Keywords | HYDROLASE / Inhibitor / Hirudin / Thrombin / Selenocysteine / Derivative | ||||||
Function / homology | Function and homology information negative regulation of serine-type peptidase activity / fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / collagen-containing extracellular matrix / serine-type endopeptidase activity ...negative regulation of serine-type peptidase activity / fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) Hirudo medicinalis (medicinal leech) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Hidmi, T. / Mousa, R. / Pomyalov, S. / Lansky, S. / Khouri, L. / Metanis, N. / Shoham, G. | ||||||
Citation | Journal: Commun Chem / Year: 2021 Title: Diselenide crosslinks for enhanced and simplified oxidative protein folding Authors: Mousa, R. / Hidmi, T. / Pomyalov, S. / Lansky, S. / Khouri, L. / Shalev, D.E. / Shoham, G. / Metanis, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a0d.cif.gz | 99.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a0d.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7a0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/7a0d ftp://data.pdbj.org/pub/pdb/validation_reports/a0/7a0d | HTTPS FTP |
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-Related structure data
Related structure data | 7a0eC 7a0fC 1hrtS 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 on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules HHHIII
#1: Protein | Mass: 29772.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00735, thrombin |
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#2: Protein | Mass: 7067.295 Da / Num. of mol.: 1 / Mutation: C16U/C28U / Source method: obtained synthetically / Source: (synth.) Hirudo medicinalis (medicinal leech) / References: UniProt: P01050 |
-Protein/peptide / Sugars , 2 types, 2 molecules LLL
#3: Protein/peptide | Mass: 5735.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00735, thrombin |
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#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 2 types, 358 molecules
#5: Chemical | ChemComp-NA / |
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#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.52 Å3/Da / Density % sol: 51.13 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 38% PEG 4000, 0.1 M sodium phosphate (pH= 4.7), 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→48.18 Å / Num. obs: 56998 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.028 / Rrim(I) all: 0.1 / Rsym value: 0.096 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 12.5 % / Rmerge(I) obs: 2.37 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2752 / CC1/2: 0.421 / Rpim(I) all: 0.693 / Rrim(I) all: 2.47 / Rsym value: 2.37 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HRT Resolution: 1.6→48.18 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.002 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.083 / ESU R Free: 0.085 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.055 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→48.18 Å
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Refine LS restraints |
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LS refinement shell |
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