+Open data
-Basic information
Entry | Database: PDB / ID: 4mhq | ||||||
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Title | Crystal structure of human primase catalytic subunit | ||||||
Components | DNA primase small subunitPrimase | ||||||
Keywords | REPLICATION / Zinc finger / Primase / NTP binding / Nucleus | ||||||
Function / homology | Function and homology information DNA primase AEP / ribonucleotide binding / DNA replication initiation / 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 / DNA primase activity / Removal of the Flap Intermediate ...DNA primase AEP / ribonucleotide binding / DNA replication initiation / 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 / DNA primase activity / 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 / magnesium ion binding / zinc ion binding / nucleoplasm / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Park, K.R. / An, J.Y. / Lee, Y. / Youn, H.S. / Lee, J.G. / Kang, J.Y. / Kim, T.G. / Lim, J.J. / Eom, S.H. / Wang, J. | ||||||
Citation | Journal: To be Published Title: Crystal structure of human primase catalytic subunit Authors: Park, K.R. / An, J.Y. / Lee, Y. / Youn, H.S. / Lee, J.G. / Kang, J.Y. / Kim, T.G. / Lim, J.J. / Eom, S.H. / Wang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mhq.cif.gz | 180.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mhq.ent.gz | 143.5 KB | Display | PDB format |
PDBx/mmJSON format | 4mhq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/4mhq ftp://data.pdbj.org/pub/pdb/validation_reports/mh/4mhq | 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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-Components
#1: Protein | Mass: 50384.469 Da / Num. of mol.: 1 / Fragment: Full length Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM1 / Plasmid: Modified pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P49642, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CIT / |
#4: 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: 2.63 Å3/Da / Density % sol: 53.25 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1M Na-acetate, 0.2M Tri-Na-citrate, 20% PEG3350, 0.1M Na-acetate , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1.28262 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jan 19, 2013 |
Radiation | Monochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28262 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 27910 / Num. obs: 25240 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.976 / Mean I/σ(I) obs: 1.506 / Num. unique all: 1263 / Rsym value: 0.976 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→38.06 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.342 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.307 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 38.961 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→38.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 18.7984 Å / Origin y: 26.7721 Å / Origin z: 53.0541 Å
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