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Yorodumi- PDB-4cs8: Crystal structure of the asymmetric human metapneumovirus M2-1 te... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cs8 | ||||||
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Title | Crystal structure of the asymmetric human metapneumovirus M2-1 tetramer, form 2 | ||||||
Components | (M2-1) x 2 | ||||||
Keywords | VIRAL PROTEIN / ANTITERMINATOR / TRANSCRIPTION ELONGATION / RNA-BINDING / MODULAR PROTEIN / ASYMMETRIC TETRAMER | ||||||
Function / homology | Function and homology information regulation of viral transcription / translation elongation factor activity / virion component / host cell cytoplasm / nucleotide binding / host cell nucleus / structural molecule activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | HUMAN METAPNEUMOVIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Leyrat, C. / Renner, M. / Harlos, K. / Grimes, J.M. | ||||||
Citation | Journal: Elife / Year: 2014 Title: Drastic Changes in Conformational Dynamics of the Antiterminator M2-1 Regulate Transcription Efficiency in Pneumovirinae. Authors: Leyrat, C. / Renner, M. / Harlos, K. / Huiskonen, J.T. / 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 | 4cs8.cif.gz | 274.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cs8.ent.gz | 224.7 KB | Display | PDB format |
PDBx/mmJSON format | 4cs8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/4cs8 ftp://data.pdbj.org/pub/pdb/validation_reports/cs/4cs8 | HTTPS FTP |
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-Related structure data
Related structure data | 4cs7SC 4cs9C 4csaC 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: 21434.266 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: ZN ION COORDINATED BY C7, C15, C21 AND H25 / Source: (gene. exp.) HUMAN METAPNEUMOVIRUS / Strain: NL1-00 (A1) / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: Q8QN58 #2: Protein | | Mass: 21435.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ZN ION COORDINATED BY C7, C15, C21 AND H25 / Source: (gene. exp.) HUMAN METAPNEUMOVIRUS / Strain: NL1-00 (A1) / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: Q8QN58 #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 48.3 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 28 % W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000, 0.100 M BIS-TRIS PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2013 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→44.81 Å / Num. obs: 45494 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Biso Wilson estimate: 46.46 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CS7 Resolution: 2.1→30.75 Å / Cor.coef. Fo:Fc: 0.9492 / Cor.coef. Fo:Fc free: 0.9434 / SU R Cruickshank DPI: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.196 / SU Rfree Blow DPI: 0.161 / SU Rfree Cruickshank DPI: 0.162
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Displacement parameters | Biso mean: 62.5 Å2
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Refine analyze | Luzzati coordinate error obs: 0.295 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 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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