+Open data
-Basic information
Entry | Database: PDB / ID: 4bwp | ||||||
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Title | Structure of Drosophila Melanogaster PAN3 pseudokinase | ||||||
Components | PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN-3 | ||||||
Keywords | GENE REGULATION / DEADENYLASE / PAN2 / MIRNA / MRNA DECAY | ||||||
Function / homology | Function and homology information : / PAN complex / positive regulation of cytoplasmic mRNA processing body assembly / : / nuclear-transcribed mRNA poly(A) tail shortening / deadenylation-dependent decapping of nuclear-transcribed mRNA / P-body / mRNA processing / protein phosphorylation / RNA binding ...: / PAN complex / positive regulation of cytoplasmic mRNA processing body assembly / : / nuclear-transcribed mRNA poly(A) tail shortening / deadenylation-dependent decapping of nuclear-transcribed mRNA / P-body / mRNA processing / protein phosphorylation / RNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | ||||||
Authors | Christie, M. / Boland, A. / Huntzinger, E. / Weichenrieder, O. / Izaurralde, E. | ||||||
Citation | Journal: Mol.Cell / Year: 2013 Title: Structure of the Pan3 Pseudokinase Reveals the Basis for Interactions with the Pan2 Deadenylase and the Gw182 Proteins Authors: Christie, M. / Boland, A. / Huntzinger, E. / Weichenrieder, O. / Izaurralde, E. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bwp.cif.gz | 323.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bwp.ent.gz | 266.9 KB | Display | PDB format |
PDBx/mmJSON format | 4bwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bwp_validation.pdf.gz | 993.5 KB | Display | wwPDB validaton report |
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Full document | 4bwp_full_validation.pdf.gz | 1021.2 KB | Display | |
Data in XML | 4bwp_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 4bwp_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/4bwp ftp://data.pdbj.org/pub/pdb/validation_reports/bw/4bwp | HTTPS FTP |
-Related structure data
Related structure data | 4bwkSC 4bwxC 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.881, -0.457, 0.122), Vector: |
-Components
#1: Protein | Mass: 50989.195 Da / Num. of mol.: 2 Fragment: PSEUDOKINSE DOMAIN, COILED COIL, CTERMINAL KNOB, RESIDUES 349-790 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PNYC-NPM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q95RR8 #2: Chemical | |
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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: 3.45 Å3/Da / Density % sol: 64 % / Description: NONE |
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Crystal grow | pH: 6.8 Details: 220 MM NA-CITRATE PH 7.0, HEPES PH 6.8, 2% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→48.8 Å / Num. obs: 17015 / % possible obs: 99.8 % / Observed criterion σ(I): 2.1 / Redundancy: 6.4 % / Biso Wilson estimate: 113 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 3.6→3.79 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BWK Resolution: 3.6→48.8 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / SU B: 75.901 / SU ML: 0.513 / Cross valid method: THROUGHOUT / ESU R Free: 0.602 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 135.648 Å2
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Refinement step | Cycle: LAST / Resolution: 3.6→48.8 Å
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Refine LS restraints |
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