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Yorodumi- PDB-1tpx: Ovine recombinant PrP(114-234), ARQ variant in complex with the F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tpx | ||||||
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Title | Ovine recombinant PrP(114-234), ARQ variant in complex with the Fab of the VRQ14 antibody | ||||||
Components |
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Keywords | UNKNOWN FUNCTION / prion / antibody | ||||||
Function / homology | Function and homology information : / : / type 5 metabotropic glutamate receptor binding / cuprous ion binding / : / positive regulation of protein tyrosine kinase activity / side of membrane / inclusion body / cellular response to copper ion / tubulin binding ...: / : / type 5 metabotropic glutamate receptor binding / cuprous ion binding / : / positive regulation of protein tyrosine kinase activity / side of membrane / inclusion body / cellular response to copper ion / tubulin binding / protein destabilization / protein homooligomerization / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / amyloid-beta binding / microtubule binding / nuclear membrane / membrane raft / copper ion binding / dendrite / protein-containing complex binding / Golgi apparatus / cell surface / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Ovis aries (sheep) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | Eghiaian, F. / Grosclaude, J. / Lesceu, S. / Debey, P. / Doublet, B. / Treguer, E. / Rezaei, H. / Knossow, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Insight into the PrPC -> PrPSc conversion from the structures of antibody-bound ovine prion scrapie-susceptibility variants. Authors: Eghiaian, F. / Grosclaude, J. / Lesceu, S. / Debey, P. / Doublet, B. / Treguer, E. / Rezaei, H. / Knossow, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tpx.cif.gz | 112.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tpx.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 1tpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/1tpx ftp://data.pdbj.org/pub/pdb/validation_reports/tp/1tpx | HTTPS FTP |
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-Related 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: 13865.371 Da / Num. of mol.: 1 / Fragment: OvPrP (114-234) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ovis aries (sheep) / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q6V654, UniProt: P23907*PLUS |
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#2: Antibody | Mass: 22810.455 Da / Num. of mol.: 1 / Fragment: residues (1-223) / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#3: Antibody | Mass: 24155.863 Da / Num. of mol.: 1 / Fragment: residues (1-214) / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#4: 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: 2.4 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: Sodium citrate 0.1M, PEG8000, Ammonium acetate 0.2M, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979774 Å |
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Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 5, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979774 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→30 Å / Num. all: 18975 / Num. obs: 18975 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 55.1 |
Reflection shell | Resolution: 2.55→2.61 Å / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 12 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→14.97 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1470639.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.9829 Å2 / ksol: 0.348243 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.56→14.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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