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Yorodumi- PDB-3ppy: Crystal structure of the D1596A/N1602A double mutant of an engine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ppy | ||||||
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Title | Crystal structure of the D1596A/N1602A double mutant of an engineered VWF A2 domain (N1493C and C1670S) | ||||||
Components | von Willebrand factor | ||||||
Keywords | CELL ADHESION / von Willebrand factor / VWA domain / and calcium / Rossmann fold / blood coagulation / protein unfolding / and ADAMTS13 cleavage / glycosylation | ||||||
Function / homology | Function and homology information Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Weibel-Palade body / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen ...Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Weibel-Palade body / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / immunoglobulin binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / extracellular matrix / platelet alpha granule lumen / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet activation / response to wounding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / blood coagulation / integrin binding / Platelet degranulation / protein-folding chaperone binding / collagen-containing extracellular matrix / protease binding / cell adhesion / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Zhou, M. / Dong, X. / Zhong, C. / Ding, J. | ||||||
Citation | Journal: Blood / Year: 2011 Title: A novel calcium-binding site of von Willebrand factor A2 domain regulates its cleavage by ADAMTS13 Authors: Zhou, M. / Dong, X. / Baldauf, C. / Chen, H. / Zhou, Y. / Springer, T.A. / Luo, X. / Zhong, C. / Grater, F. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ppy.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ppy.ent.gz | 65.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ppy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ppy_validation.pdf.gz | 424.4 KB | Display | wwPDB validaton report |
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Full document | 3ppy_full_validation.pdf.gz | 425 KB | Display | |
Data in XML | 3ppy_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 3ppy_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/3ppy ftp://data.pdbj.org/pub/pdb/validation_reports/pp/3ppy | HTTPS FTP |
-Related structure data
Related structure data | 3ppvSC 3ppwC 3ppxC 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
#1: Protein | Mass: 21976.791 Da / Num. of mol.: 1 / Fragment: VWF A2 domain, UNP residues 1488-1674 / Mutation: N1493, D1596A, N1602A, C1670S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F8VWF, VWF / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: P04275 |
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#2: Chemical | ChemComp-NA / |
#3: 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: 2.63 Å3/Da / Density % sol: 53.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 0.1M sodium citrate, 1.6M (NH4)2SO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: May 10, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 15351 / % possible obs: 99.3 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 3.4 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PPV Resolution: 2→36.26 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0.8 / SU B: 8.071 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.798 Å2
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Refinement step | Cycle: LAST / Resolution: 2→36.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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