+Open data
-Basic information
Entry | Database: PDB / ID: 6vg6 | ||||||
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Title | Crystal structure of DPO4 with 8-oxoadenine (oxoA) and dGTP* | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Y-family DNA polymerase / Translesion synthesis / TRANSFERASE / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharolobus solfataricus (archaea) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å | ||||||
Authors | Jung, H. / Lee, S. | ||||||
Citation | Journal: Biochem.J. / Year: 2020 Title: Promutagenic bypass of 7,8-dihydro-8-oxoadenine by translesion synthesis DNA polymerase Dpo4. Authors: Jung, H. / Lee, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vg6.cif.gz | 187.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vg6.ent.gz | 142.6 KB | Display | PDB format |
PDBx/mmJSON format | 6vg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vg6_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6vg6_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6vg6_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 6vg6_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/6vg6 ftp://data.pdbj.org/pub/pdb/validation_reports/vg/6vg6 | HTTPS FTP |
-Related structure data
Related structure data | 6vgmC 1jx4S 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
-DNA chain , 2 types, 4 molecules PBTC
#1: DNA chain | Mass: 4096.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #2: DNA chain | Mass: 5387.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Protein , 1 types, 2 molecules AD
#3: Protein | Mass: 39019.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharolobus solfataricus (archaea) Gene: dbh, SSOP1_2570, SULA_0242, SULB_0243, SULC_0242, SULG_01230, SULH_01230, SULI_01230, SULM_01230, SULN_01230, SULO_01240, SULZ_01250 Production host: Escherichia coli (E. coli) References: UniProt: A0A0E3K6E9, UniProt: Q97W02*PLUS, DNA-directed DNA polymerase |
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-Non-polymers , 4 types, 30 molecules
#4: Chemical | #5: Chemical | ChemComp-MG / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.7 Å3/Da / Density % sol: 54.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 16% PEG3350 50 mM Tris 100 mM Magnesium acetate |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.08→50 Å / Num. obs: 19085 / % possible obs: 98.6 % / Redundancy: 3.3 % / Rpim(I) all: 0.059 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 3.08→3.14 Å / Num. unique obs: 1027 / CC1/2: 0.486 / Rpim(I) all: 0.461 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JX4 Resolution: 3.08→45.15 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 72.88 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.08→45.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.08→3.24 Å
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