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Yorodumi- PDB-3pq1: Crystal structure of human mitochondrial poly(A) polymerase (PAPD1) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pq1 | ||||||
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Title | Crystal structure of human mitochondrial poly(A) polymerase (PAPD1) | ||||||
Components | Poly(A) RNA polymerase | ||||||
Keywords | TRANSFERASE / nucleotidyl transferase / RNP-type RNA binding domain / poly(A) polymerase / mitochondria | ||||||
Function / homology | Function and homology information : / polynucleotide adenylyltransferase / histone mRNA catabolic process / UTP binding / : / nucleotidyltransferase activity / mRNA processing / manganese ion binding / intracellular membrane-bounded organelle / magnesium ion binding ...: / polynucleotide adenylyltransferase / histone mRNA catabolic process / UTP binding / : / nucleotidyltransferase activity / mRNA processing / manganese ion binding / intracellular membrane-bounded organelle / magnesium ion binding / protein homodimerization activity / mitochondrion / RNA binding / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å | ||||||
Authors | Bai, Y. / Srivastava, S.K. / Chang, J.H. / Tong, L. | ||||||
Citation | Journal: Mol.Cell / Year: 2011 Title: Structural basis for dimerization and activity of human PAPD1, a noncanonical poly(A) polymerase. Authors: Bai, Y. / Srivastava, S.K. / Chang, J.H. / Manley, J.L. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pq1.cif.gz | 281.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pq1.ent.gz | 235.6 KB | Display | PDB format |
PDBx/mmJSON format | 3pq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/3pq1 ftp://data.pdbj.org/pub/pdb/validation_reports/pq/3pq1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 52330.375 Da / Num. of mol.: 2 / Mutation: D325A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MTPAP, PAPD1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta (DE3) References: UniProt: Q9NVV4, polynucleotide adenylyltransferase Sequence details | AMINO ACID SEQUENCE CORRESPONDING TO RESIDUES 44-538 IN UNIPROT DATABASE ENTRY Q9NVV4, PLUS A N- ...AMINO ACID SEQUENCE CORRESPOND | |
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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: 2.15 Å3/Da / Density % sol: 42.8 % |
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Crystal grow | Temperature: 293 K / Method: microbatch Details: The precipitant solution contained 100 mM MES (pH 6.0), 6% (v/v) PEG4000, 35 mM NaCl, and 5 mM MgSO4. The protein was at 20 mg/mL concentration, and 0.5 mM MgATP was included as an additive. ...Details: The precipitant solution contained 100 mM MES (pH 6.0), 6% (v/v) PEG4000, 35 mM NaCl, and 5 mM MgSO4. The protein was at 20 mg/mL concentration, and 0.5 mM MgATP was included as an additive., microbatch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.96863, 0.97888, 0.97926 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Details: MIRRORS | ||||||||||||
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.1→30 Å / Num. obs: 30725 / % possible obs: 97.7 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.9681 | ||||||||||||
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 2 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 2.342 / % possible all: 90.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.1→28.912 Å / SU ML: 0.62 / σ(F): 1.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.119 Å2 / ksol: 0.272 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.1→28.912 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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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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