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Yorodumi- PDB-3bjy: Catalytic core of Rev1 in complex with DNA (modified template gua... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bjy | |||||||||
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Title | Catalytic core of Rev1 in complex with DNA (modified template guanine) and incoming nucleotide | |||||||||
Components |
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Keywords | Transferase/DNA / DNA Polymerase / Protein-DNA complex / adduct / bypass / DNA damage / DNA repair / DNA synthesis / DNA-binding / Magnesium / Metal-binding / Nucleotidyltransferase / Nucleus / Transferase / Transferase-DNA COMPLEX | |||||||||
Function / homology | Function and homology information deoxycytidyl transferase activity / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / error-free translesion synthesis / error-prone translesion synthesis / replication fork / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / damaged DNA binding ...deoxycytidyl transferase activity / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / error-free translesion synthesis / error-prone translesion synthesis / replication fork / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / damaged DNA binding / DNA-directed DNA polymerase activity / chromatin / mitochondrion / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | |||||||||
Authors | Nair, D.T. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K. | |||||||||
Citation | Journal: Structure / Year: 2008 Title: Protein-template-directed synthesis across an acrolein-derived DNA adduct by yeast Rev1 DNA polymerase Authors: Nair, D.T. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bjy.cif.gz | 120.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bjy.ent.gz | 88.2 KB | Display | PDB format |
PDBx/mmJSON format | 3bjy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bjy_validation.pdf.gz | 844.4 KB | Display | wwPDB validaton report |
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Full document | 3bjy_full_validation.pdf.gz | 857.7 KB | Display | |
Data in XML | 3bjy_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 3bjy_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/3bjy ftp://data.pdbj.org/pub/pdb/validation_reports/bj/3bjy | HTTPS FTP |
-Related structure data
Related structure data | 2aq4S S: Starting model for refinement |
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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: 49452.965 Da / Num. of mol.: 1 / Fragment: catalytic core Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: REV1 / Plasmid: pBJ954 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5464 References: UniProt: P12689, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 5107.365 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 3502.308 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 161 molecules
#4: Chemical | ChemComp-DCP / | ||
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#5: Chemical | #6: 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: 4.35 Å3/Da / Density % sol: 71.74 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16% PEG 5K MME, 0.4M Ammonoium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 18, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→50 Å / Num. obs: 38556 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 32.1 |
Reflection shell | Resolution: 2.41→2.5 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 8.8 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AQ4 Resolution: 2.41→50 Å / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.41→50 Å
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