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Yorodumi- PDB-4bxt: Crystal structure of the human metapneumovirus phosphoprotein tet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bxt | ||||||
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Title | Crystal structure of the human metapneumovirus phosphoprotein tetramerization domain | ||||||
Components | PHOSPHOPROTEIN P | ||||||
Keywords | VIRAL PROTEIN / TETRAMERIC PARALLEL COILED COIL | ||||||
Function / homology | Phosphoprotein, pneumoviral / Pneumovirus phosphoprotein / RNA-dependent RNA polymerase activity / Phosphoprotein Function and homology information | ||||||
Biological species | HUMAN METAPNEUMOVIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å | ||||||
Authors | Leyrat, C. / Renner, M. / Harlos, K. / Grimes, J.M. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Solution and Crystallographic Structures of the Central Region of the Phosphoprotein from Human Metapneumovirus Authors: Leyrat, C. / Renner, M. / Harlos, K. / Grimes, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bxt.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bxt.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 4bxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bxt_validation.pdf.gz | 472.5 KB | Display | wwPDB validaton report |
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Full document | 4bxt_full_validation.pdf.gz | 478.4 KB | Display | |
Data in XML | 4bxt_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 4bxt_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/4bxt ftp://data.pdbj.org/pub/pdb/validation_reports/bx/4bxt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.941234, 0.205036, -0.2684), Vector: |
-Components
#1: Protein | Mass: 8773.052 Da / Num. of mol.: 8 / Fragment: TETRAMERIZATION DOMAIN, RESIDUES 158-237 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN METAPNEUMOVIRUS / Strain: SEROTYPE A1 (NL/1/00) / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: Q91KZ5 |
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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: 2.4 Å3/Da / Density % sol: 39.7 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 25 % PEG 3350, 100 MM HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92001 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2013 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92001 Å / Relative weight: 1 |
Reflection | Resolution: 3.13→66.91 Å / Num. obs: 3602 / % possible obs: 90.3 % / Observed criterion σ(I): 1.5 / Redundancy: 10.5 % / Biso Wilson estimate: 77.44 Å2 / Rmerge(I) obs: 0.35 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 3.13→3.21 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.35 / Mean I/σ(I) obs: 1.4 / % possible all: 57.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SAXS-FILTERED ROSETTA FOLD-AND-DOCK AB INITIO MODEL Resolution: 3.13→46.42 Å / Cor.coef. Fo:Fc: 0.8587 / Cor.coef. Fo:Fc free: 0.7759 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.542
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Displacement parameters | Biso mean: 53.43 Å2
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Refine analyze | Luzzati coordinate error obs: 0.706 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.13→46.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.13→3.5 Å / Total num. of bins used: 5
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Refinement TLS params. | S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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