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Yorodumi- PDB-1im4: Crystal Structure of a DinB Homolog (DBH) Lesion Bypass DNA Polym... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1im4 | ||||||
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Title | Crystal Structure of a DinB Homolog (DBH) Lesion Bypass DNA Polymerase Catalytic Fragment from Sulfolobus solfataricus | ||||||
Components | DBH | ||||||
Keywords | TRANSFERASE / DNA polymerase palm / thumb / fingers / helix-hairpin-helix / fidelity / processivity | ||||||
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 | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Pata, J.D. / Zhou, B.L. / Steitz, T.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2001 Title: Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain. Authors: Zhou, B.L. / Pata, J.D. / Steitz, T.A. #1: Journal: Mutat.Res. / Year: 1996 Title: Identification of a DinB/UmuC Homolog in the Archeon Sulfolobus solfataricus Authors: Kulaeva, O.I. / Koonin, E.V. / McDonald, J.P. / Randall, S.K. / Rabinovich, N. / Connaughton, J.F. / Levine, A.S. / Woodgate, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1im4.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1im4.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 1im4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1im4_validation.pdf.gz | 438.5 KB | Display | wwPDB validaton report |
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Full document | 1im4_full_validation.pdf.gz | 442.5 KB | Display | |
Data in XML | 1im4_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 1im4_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/1im4 ftp://data.pdbj.org/pub/pdb/validation_reports/im/1im4 | HTTPS FTP |
-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: 24836.789 Da / Num. of mol.: 1 / Fragment: N-terminal catalytic domain (residues 2-216) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: DBH / Plasmid: pNHis-DBH-216 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)pLysS / References: UniProt: P96022, DNA-directed DNA polymerase | ||
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#2: Chemical | #3: 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: 2.9 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonium sulfate, magnesium chloride, MPD, Tris-HCl, beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Aug 16, 2000 / Details: double crystal monochromator |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 12897 / Num. obs: 12897 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 38.4 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 3.8 / Num. unique all: 849 / % possible all: 97.8 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 97.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→28.91 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1260659.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 Stereochemistry target values: Engh & Huber, as implemented in CNS
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.12 Å2 / ksol: 0.31 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→28.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 8.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 52.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.305 / % reflection Rfree: 4.3 % / Rfactor Rwork: 0.323 |