+Open data
-Basic information
Entry | Database: PDB / ID: 4p37 | ||||||
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Title | Crystal structure of the Megavirus polyadenylate synthase | ||||||
Components | (Putative poly(A) polymerase catalytic ...) x 2 | ||||||
Keywords | TRANSFERASE / PolyA polymerase | ||||||
Function / homology | Poly(A) polymerase catalytic subunit / DI(HYDROXYETHYL)ETHER / Putative poly(A) polymerase catalytic subunit Function and homology information | ||||||
Biological species | Megavirus chiliensis | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.24 Å | ||||||
Authors | Priet, S. / Lartigue, A. / Claverie, J.M. / Abergel, C. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2015 Title: mRNA maturation in giant viruses: variation on a theme. Authors: Priet, S. / Lartigue, A. / Debart, F. / Claverie, J.M. / Abergel, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p37.cif.gz | 231.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p37.ent.gz | 192.4 KB | Display | PDB format |
PDBx/mmJSON format | 4p37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/4p37 ftp://data.pdbj.org/pub/pdb/validation_reports/p3/4p37 | 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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Details | Gel filtration confirms the dimerization of the protein in solution |
-Components
-Putative poly(A) polymerase catalytic ... , 2 types, 2 molecules AB
#1: Protein | Mass: 63666.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Megavirus chiliensis / Gene: mg561 / Plasmid: modified pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: G5CT11 |
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#2: Protein | Mass: 63707.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Megavirus chiliensis / Gene: mg561 / Plasmid: modified pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: G5CT11 |
-Non-polymers , 4 types, 592 molecules
#3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-TRS / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.1M Tris-HCl, PEG 200 |
-Data collection
Diffraction | Mean temperature: 105 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793, 0.9795, 0.9770 | ||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2011 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.24→51.3 Å / Num. obs: 62550 / % possible obs: 99 % / Redundancy: 3.9 % / Biso Wilson estimate: 49.16 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 6.7 | ||||||||||||
Reflection shell | Resolution: 2.24→2.36 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.5 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.24→49.38 Å / Cor.coef. Fo:Fc: 0.9351 / Cor.coef. Fo:Fc free: 0.9181 / SU R Cruickshank DPI: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.255 / SU Rfree Blow DPI: 0.184 / SU Rfree Cruickshank DPI: 0.183
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Displacement parameters | Biso mean: 55.14 Å2
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Refine analyze | Luzzati coordinate error obs: 0.276 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→49.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.24→2.3 Å / Total num. of bins used: 20
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