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Yorodumi- PDB-5dqo: Crystal structure of Y347F mutant of human primase p58 iron-sulfu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dqo | ||||||
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Title | Crystal structure of Y347F mutant of human primase p58 iron-sulfur cluster domain | ||||||
Components | DNA primase large subunitPrimase | ||||||
Keywords | REPLICATION / Iron-Sulfur Cluster / DNA Priming | ||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Salay, L.E. / Thompson, M.K. / Chazin, W.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2017 Title: The [4Fe4S] cluster of human DNA primase functions as a redox switch using DNA charge transport. Authors: O'Brien, E. / Holt, M.E. / Thompson, M.K. / Salay, L.E. / Ehlinger, A.C. / Chazin, W.J. / Barton, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dqo.cif.gz | 138.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dqo.ent.gz | 105.9 KB | Display | PDB format |
PDBx/mmJSON format | 5dqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/5dqo ftp://data.pdbj.org/pub/pdb/validation_reports/dq/5dqo | HTTPS FTP |
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-Related structure data
Related structure data | 5i7mC 3l9qS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22655.949 Da / Num. of mol.: 4 / Fragment: p58C domain (UNP residues 272-464) / Mutation: Y347F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM2, PRIM2A / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P49643, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: Chemical | ChemComp-SF4 / #3: 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: 2.87 Å3/Da / Density % sol: 57.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 300 mM lithium sulfate, 100 mM Tris, pH 8.5, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 4.5 % / Number: 184871 / Rmerge(I) obs: 0.058 / Χ2: 1.76 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 41462 / % possible obs: 92.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection twin |
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Reflection | Resolution: 2.3→82.243 Å / Num. all: 44770 / Num. obs: 42683 / % possible obs: 92.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.058 / Net I/av σ(I): 27.591 / Net I/σ(I): 12.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | Packing: 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3L9Q Resolution: 2.3→44.14 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.743 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.048 / 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: 54.343 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→44.14 Å
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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