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Yorodumi- PDB-3l9q: Crystal structure of human polymerase alpha-primase p58 iron-sulf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l9q | ||||||
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Title | Crystal structure of human polymerase alpha-primase p58 iron-sulfur cluster domain | ||||||
Components | DNA primase large subunitPrimase | ||||||
Keywords | TRANSFERASE / pol alpha / primase / DNA replication / polymerase / iron-sulfur cluster / DNA-binding / DNA-directed RNA polymerase / Iron / Iron-sulfur / Metal-binding / Nucleotidyltransferase / Phosphoprotein / Primosome / Transcription | ||||||
Function / homology | Function and homology information positive regulation of DNA primase activity / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere ...positive regulation of DNA primase activity / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / DNA replication, synthesis of primer / Activation of the pre-replicative complex / DNA replication initiation / Defective pyroptosis / 4 iron, 4 sulfur cluster binding / DNA binding / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.698 Å | ||||||
Authors | Vaithiyalingam, S. / Eichman, B.F. / Chazin, W.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Insights into eukaryotic DNA priming from the structure and functional interactions of the 4Fe-4S cluster domain of human DNA primase. Authors: Vaithiyalingam, S. / Warren, E.M. / Eichman, B.F. / Chazin, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l9q.cif.gz | 171 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l9q.ent.gz | 144.4 KB | Display | PDB format |
PDBx/mmJSON format | 3l9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/3l9q ftp://data.pdbj.org/pub/pdb/validation_reports/l9/3l9q | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22517.781 Da / Num. of mol.: 2 / Fragment: iron-sulfur cluster domain (UNP residues 272-464) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM2, PRIM2A / Production host: Escherichia coli (E. coli) References: UniProt: P49643, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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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: 2.59 Å3/Da / Density % sol: 52.57 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, 15% PEG 3250, 0.2 M LiSO4, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 160 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 17, 2009 |
Radiation | Monochromator: C111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→46.8 Å / Num. all: 49696 / Num. obs: 49683 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 16.8 Å2 / Rsym value: 0.074 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 6.9 / Num. unique all: 4301 / Rsym value: 0.238 / % possible all: 84.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.698→37.321 Å / SU ML: 0.39 / σ(F): 1.34 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.484 Å2 / ksol: 0.368 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.698→37.321 Å
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Refine LS restraints |
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LS refinement shell |
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