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Yorodumi- PDB-4dl4: Human DNA polymerase eta inserting dCMPNPP opposite the 3'G of ci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dl4 | ||||||
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Title | Human DNA polymerase eta inserting dCMPNPP opposite the 3'G of cisplatin crosslinked Gs (Pt-GG1). | ||||||
Components |
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Keywords | TRANSFERASE/DNA/INHIBITOR / cisplatin / chemoresistence / translesion synthesis / human DNA polymerse eta / kinetics / molecular splint / inhibition / DNA distorsion / second TLS polymerase / nucleotidyl transfer reaction / PCNA / TRANSFERASE-DNA-INHIBITOR complex | ||||||
Function / homology | Function and homology information response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / cellular response to UV-C / pyrimidine dimer repair / regulation of DNA repair / error-prone translesion synthesis / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH ...response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / cellular response to UV-C / pyrimidine dimer repair / regulation of DNA repair / error-prone translesion synthesis / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / response to radiation / HDR through Homologous Recombination (HRR) / site of double-strand break / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Zhao, Y. / Biertumpfel, C. / Gregory, M. / Hua, Y.-J. / Hanaoka, F. / Yang, W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural Basis for Chemoresistance to Cisplatin Mediated by DNA Polymerase eta Authors: Zhao, Y. / Biertumpfel, C. / Gregory, M.T. / Hua, Y.J. / Hanaoka, F. / Yang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dl4.cif.gz | 124 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dl4.ent.gz | 90.3 KB | Display | PDB format |
PDBx/mmJSON format | 4dl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dl4_validation.pdf.gz | 825.7 KB | Display | wwPDB validaton report |
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Full document | 4dl4_full_validation.pdf.gz | 837.4 KB | Display | |
Data in XML | 4dl4_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 4dl4_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/4dl4 ftp://data.pdbj.org/pub/pdb/validation_reports/dl/4dl4 | HTTPS FTP |
-Related structure data
Related structure data | 4dl2C 4dl3C 4dl5C 4dl6C 4dl7C 3mr2S 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48617.707 Da / Num. of mol.: 1 / Fragment: unp residues 1-432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLH, RAD30, RAD30A, XPV / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) plysS / References: UniProt: Q9Y253, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 3004.981 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 2810.858 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: dCMPNPP |
-Non-polymers , 5 types, 214 molecules
#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-CPT / | #7: Chemical | ChemComp-0KX / | #8: 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: 2.14 Å3/Da / Density % sol: 42.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MES, MgCl2, PEG 2K-MME, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 15, 2010 Details: double Si(220) crystal and mirror vertical focusing | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double Si(220) crystal and mirror vertical focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→30 Å / Num. all: 30655 / Num. obs: 30558 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 21.51 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.12 / Net I/σ(I): 11.33 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MR2 Resolution: 2→30 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8742 / SU ML: 0.59 / σ(F): 1.36 / σ(I): 0 / Phase error: 20.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.054 Å2 / ksol: 0.335 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.16 Å2 / Biso mean: 26.8717 Å2 / Biso min: 7.23 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17
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