+Open data
-Basic information
Entry | Database: PDB / ID: 3b4d | ||||||
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Title | Crystal Structure of Human PABPN1 RRM | ||||||
Components | Polyadenylate-binding protein 2 | ||||||
Keywords | RNA BINDING PROTEIN / RRM fold / ALPHA-BETA Sandwich structure / RNA Binding Domain / RNA Recognition Motif / Acetylation / Alternative splicing / Coiled coil / Cytoplasm / Disease mutation / Methylation / mRNA processing / Nucleus / Polymorphism / RNA-binding / Triplet repeat expansion | ||||||
Function / homology | Function and homology information positive regulation of polynucleotide adenylyltransferase activity / Inhibition of Host mRNA Processing and RNA Silencing / Processing of Intronless Pre-mRNAs / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / nuclear inclusion body / poly(A) binding / mRNA 3'-end processing / RNA polymerase binding / RNA Polymerase II Transcription Termination / poly(A)+ mRNA export from nucleus ...positive regulation of polynucleotide adenylyltransferase activity / Inhibition of Host mRNA Processing and RNA Silencing / Processing of Intronless Pre-mRNAs / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / nuclear inclusion body / poly(A) binding / mRNA 3'-end processing / RNA polymerase binding / RNA Polymerase II Transcription Termination / poly(A)+ mRNA export from nucleus / Processing of Capped Intron-Containing Pre-mRNA / RNA processing / muscle contraction / mRNA processing / MAPK cascade / cellular response to lipopolysaccharide / nuclear speck / ribonucleoprotein complex / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 2.001 Å | ||||||
Authors | Ge, H. / Tong, S. / Teng, M. / Niu, L. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure and possible dimerization of the single RRM of human PABPN1 Authors: Ge, H. / Zhou, D. / Tong, S. / Gao, Y. / Teng, M. / Niu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b4d.cif.gz | 30 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b4d.ent.gz | 19.9 KB | Display | PDB format |
PDBx/mmJSON format | 3b4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/3b4d ftp://data.pdbj.org/pub/pdb/validation_reports/b4/3b4d | 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: 10861.189 Da / Num. of mol.: 1 / Fragment: UNP residues 167-254 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PABPN1, PAB2, PABP2 / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q86U42 |
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#2: 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: 3.02 Å3/Da / Density % sol: 59.29 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, 4.2M sodium chloride, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 10, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.001→65.233 Å / Num. obs: 9002 / Redundancy: 12.7 % / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 2.001→2.07 Å / Redundancy: 12.7 % |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.001→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.789 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.123 / 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: 34.155 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.001→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.002→2.053 Å / Total num. of bins used: 20
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