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Yorodumi- PDB-8oxr: Structure of the N-terminal didomain d1_d2 of the Thrombospondin ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oxr | ||||||
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Title | Structure of the N-terminal didomain d1_d2 of the Thrombospondin type-1 domain-containing 7A | ||||||
Components | Thrombospondin type-1 domain-containing protein 7A | ||||||
Keywords | CELL ADHESION / Membranous Nephropathy / Thrombospondin repeat | ||||||
Function / homology | Function and homology information Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / cell projection / actin cytoskeleton organization / angiogenesis / cell differentiation / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Bochel, A. / Mortensen, S.A. / Chojnowski, G. / Wilmanns, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: Structure of the N-terminal didomain d1_d2 of the Thrombospondin type-1 domain-containing 7A Authors: Bochel, A. / Mortensen, S.A. / Seifert, L. / Hengel, F.E. / Jeffries, C.M. / Chojnowski, G. / Kretz, O. / Huber, T.B. / Tomas, N.M. / Wilmanns, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oxr.cif.gz | 65.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oxr.ent.gz | 45 KB | Display | PDB format |
PDBx/mmJSON format | 8oxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oxr_validation.pdf.gz | 403.1 KB | Display | wwPDB validaton report |
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Full document | 8oxr_full_validation.pdf.gz | 403.1 KB | Display | |
Data in XML | 8oxr_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 8oxr_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/8oxr ftp://data.pdbj.org/pub/pdb/validation_reports/ox/8oxr | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16519.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: THSD7A, KIAA0960 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9UPZ6 |
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#2: 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: 2.99 Å3/Da / Density % sol: 58.83 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium chloride, 0.1 M bis-tris, 1.5 M ammonium sulphate, pH 6.5 |
-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: P14 (MX2) / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Aug 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→57.56 Å / Num. obs: 9135 / % possible obs: 99.8 % / Redundancy: 13.2 % / CC1/2: 1 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 855 / CC1/2: 0.62 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→57.555 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.259 / WRfactor Rwork: 0.197 / SU B: 10.481 / SU ML: 0.226 / Average fsc free: 0.9211 / Average fsc work: 0.941 / Cross valid method: FREE R-VALUE / ESU R: 0.263 / ESU R Free: 0.24 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: 58.873 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→57.555 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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