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Yorodumi- PDB-5hvg: Crystal Structure of Thrombin-activatable Fibrinolysis Inhibitor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hvg | |||||||||
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Title | Crystal Structure of Thrombin-activatable Fibrinolysis Inhibitor in Complex with an Inhibitory Nanobody (VHH-a204) | |||||||||
Components |
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Keywords | hydrolase/hydrolase inhibitor / procarboxypeptidase U / thrombin-activatable fibrinolysis inhibitor / TAFI / procarboxypeptidase R / plasma procarboxypeptidase B / nanobody / antibody fragment / protein complex / hydrolase-hydrolase inhibitor complex | |||||||||
Function / homology | Function and homology information carboxypeptidase U / positive regulation of extracellular matrix constituent secretion / negative regulation of hepatocyte proliferation / negative regulation of plasminogen activation / negative regulation of fibrinolysis / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / fibrinolysis / Regulation of Complement cascade / liver regeneration ...carboxypeptidase U / positive regulation of extracellular matrix constituent secretion / negative regulation of hepatocyte proliferation / negative regulation of plasminogen activation / negative regulation of fibrinolysis / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / fibrinolysis / Regulation of Complement cascade / liver regeneration / cellular response to glucose stimulus / protein catabolic process / blood coagulation / response to xenobiotic stimulus / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Vicugna pacos (alpaca) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.05 Å | |||||||||
Authors | Zhou, X. / Weeks, S.D. / Strelkov, S.V. / Declerck, P.J. | |||||||||
Funding support | Belgium, 1items
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Citation | Journal: J.Thromb.Haemost. / Year: 2016 Title: Elucidation of the molecular mechanisms of two nanobodies that inhibit thrombin-activatable fibrinolysis inhibitor activation and activated thrombin-activatable fibrinolysis inhibitor activity. Authors: Zhou, X. / Weeks, S.D. / Ameloot, P. / Callewaert, N. / Strelkov, S.V. / Declerck, P.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hvg.cif.gz | 432.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hvg.ent.gz | 360.2 KB | Display | PDB format |
PDBx/mmJSON format | 5hvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hvg_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5hvg_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5hvg_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 5hvg_validation.cif.gz | 50.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/5hvg ftp://data.pdbj.org/pub/pdb/validation_reports/hv/5hvg | HTTPS FTP |
-Related structure data
Related structure data | 5hvfC 5hvhC 4p10S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein / Antibody , 2 types, 4 molecules ACBD
#1: Protein | Mass: 46080.176 Da / Num. of mol.: 2 / Mutation: S305C-T325I-T329I-H333Y-S335Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CPB2 / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): M5 / References: UniProt: Q96IY4, carboxypeptidase U #2: Antibody | Mass: 14034.362 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pHEN6 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 |
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-Sugars , 3 types, 6 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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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 |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 4 molecules
#6: Chemical | #7: Chemical | |
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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: 5.01 Å3/Da / Density % sol: 75.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M ammonium acetate, 0.1 M bis-Tris, 16 % w/v PEG-10k |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2014 / Details: Kirkpatrick-Baez pair of bi-morph mirrors | ||||||||||||||||||||||||||||||
Radiation | Monochromator: channel cut cryogenically cooled monochromator crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.05→48.38 Å / Num. obs: 45398 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 70.48 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.142 / Rrim(I) all: 0.279 / Net I/σ(I): 5.3 / Num. measured all: 173375 / Scaling rejects: 280 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P10 Resolution: 3.05→48.38 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.8949 / SU R Cruickshank DPI: 0.469 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.42 / SU Rfree Blow DPI: 0.268 / SU Rfree Cruickshank DPI: 0.28
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Displacement parameters | Biso max: 199.66 Å2 / Biso mean: 85.02 Å2 / Biso min: 28.1 Å2
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Refine analyze | Luzzati coordinate error obs: 0.415 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.05→48.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.05→3.13 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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