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Yorodumi- PDB-3tvj: Catalytic fragment of MASP-2 in complex with its specific inhibit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tvj | ||||||
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Title | Catalytic fragment of MASP-2 in complex with its specific inhibitor developed by directed evolution on SGCI scaffold | ||||||
Components |
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Keywords | HYDROLASE / in vitro evolution / specific inhibitor / allostery | ||||||
Function / homology | Function and homology information mannan-binding lectin-associated serine protease-2 / complement component C4b binding / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / complement activation, lectin pathway / Initial triggering of complement / complement activation, classical pathway / serine-type endopeptidase inhibitor activity / calcium-dependent protein binding / peptidase activity ...mannan-binding lectin-associated serine protease-2 / complement component C4b binding / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / complement activation, lectin pathway / Initial triggering of complement / complement activation, classical pathway / serine-type endopeptidase inhibitor activity / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity / calcium ion binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Schistocerca gregaria (desert locust) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å | ||||||
Authors | Heja, D. / Harmat, V. / Dobo, J. / Szasz, R. / Kekesi, K.A. / Zavodszky, P. / Gal, P. / Pal, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Monospecific Inhibitors Show That Both Mannan-binding Lectin-associated Serine Protease-1 (MASP-1) and -2 Are Essential for Lectin Pathway Activation and Reveal Structural Plasticity of MASP-2. Authors: Heja, D. / Harmat, V. / Fodor, K. / Wilmanns, M. / Dobo, J. / Kekesi, K.A. / Zavodszky, P. / Gal, P. / Pal, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tvj.cif.gz | 183.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tvj.ent.gz | 145.2 KB | Display | PDB format |
PDBx/mmJSON format | 3tvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tvj_validation.pdf.gz | 458.3 KB | Display | wwPDB validaton report |
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Full document | 3tvj_full_validation.pdf.gz | 464.4 KB | Display | |
Data in XML | 3tvj_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 3tvj_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/3tvj ftp://data.pdbj.org/pub/pdb/validation_reports/tv/3tvj | HTTPS FTP |
-Related structure data
Related structure data | 4djzC 1gl1S 1q3xS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9217.346 Da / Num. of mol.: 1 / Fragment: Sushi 2 domain residues 363-444 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MASP2 / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 De3 References: UniProt: O00187, mannan-binding lectin-associated serine protease-2 |
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#2: Protein | Mass: 26542.971 Da / Num. of mol.: 1 / Fragment: Peptidase S1 domain residues 445-686 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MASP2 / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 De3 References: UniProt: O00187, mannan-binding lectin-associated serine protease-2 |
#3: Protein/peptide | Mass: 4020.530 Da / Num. of mol.: 1 / Mutation: A83V, L86K, K87L, A88W, P90N Source method: isolated from a genetically manipulated source Details: expressed as MBP fusion protein / Source: (gene. exp.) Schistocerca gregaria (desert locust) / Gene: GenBank: Y09605.1 / Plasmid: pMal-TEV-SGPI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star / References: UniProt: O46162 |
#4: Chemical | ChemComp-SO4 / |
#5: 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: 46.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 24.5% PEG 5000 MME, 0.164 M ammonium sulphate, 82 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 21, 2011 | |||||||||||||||||||||
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.28→40 Å / Num. all: 90627 / Num. obs: 90627 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.44 % / Biso Wilson estimate: 16.911 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.1 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: domains of PDB entry 1Q3X, and PDB entry 1GL1 Resolution: 1.28→38 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.182 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.28→38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.28→1.313 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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