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Yorodumi- PDB-3qsb: Structure of E. coli polIIIbeta with (Z)-5-(1-((4'-Fluorobiphenyl... -
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-Basic information
Entry | Database: PDB / ID: 3qsb | ||||||
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Title | Structure of E. coli polIIIbeta with (Z)-5-(1-((4'-Fluorobiphenyl-4-yl)methoxyimino)butyl)-2,2-dimethyl-4,6-dioxocyclohexanecarbonitrile | ||||||
Components | (DNA polymerase III subunit beta) x 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / DNA replication / sliding clamp / DnaN / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity ...Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase activity / DNA damage response / protein homodimerization activity / DNA binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wijffels, G. / Johnson, W.M. / Oakley, A.J. / Turner, K. / Epa, V.C. / Briscoe, S.J. / Polley, M. / Liepa, A.J. / Hofmann, A. / Buchardt, J. ...Wijffels, G. / Johnson, W.M. / Oakley, A.J. / Turner, K. / Epa, V.C. / Briscoe, S.J. / Polley, M. / Liepa, A.J. / Hofmann, A. / Buchardt, J. / Christensen, C. / Prosselkov, P. / Dalrymple, B.P. / Alewood, P.F. / Jennings, P.A. / Dixon, N.E. / Winkler, D.A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Binding inhibitors of the bacterial sliding clamp by design Authors: Wijffels, G. / Johnson, W.M. / Oakley, A.J. / Turner, K. / Epa, V.C. / Briscoe, S.J. / Polley, M. / Liepa, A.J. / Hofmann, A. / Buchardt, J. / Christensen, C. / Prosselkov, P. / Dalrymple, B. ...Authors: Wijffels, G. / Johnson, W.M. / Oakley, A.J. / Turner, K. / Epa, V.C. / Briscoe, S.J. / Polley, M. / Liepa, A.J. / Hofmann, A. / Buchardt, J. / Christensen, C. / Prosselkov, P. / Dalrymple, B.P. / Alewood, P.F. / Jennings, P.A. / Dixon, N.E. / Winkler, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qsb.cif.gz | 170.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qsb.ent.gz | 134.2 KB | Display | PDB format |
PDBx/mmJSON format | 3qsb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qsb_validation.pdf.gz | 961.7 KB | Display | wwPDB validaton report |
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Full document | 3qsb_full_validation.pdf.gz | 1016.5 KB | Display | |
Data in XML | 3qsb_validation.xml.gz | 36.5 KB | Display | |
Data in CIF | 3qsb_validation.cif.gz | 51.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/3qsb ftp://data.pdbj.org/pub/pdb/validation_reports/qs/3qsb | HTTPS FTP |
-Related structure data
Related structure data | 1mmiS 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
#1: Protein | Mass: 40630.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dnaN / Plasmid: pND261 / Production host: Escherichia coli (E. coli) / Strain (production host): AN1459 / References: UniProt: P0A988, DNA-directed DNA polymerase | ||
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#2: Protein | Mass: 40646.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dnaN / Plasmid: pND261 / Production host: Escherichia coli (E. coli) / Strain (production host): AN1459 / References: UniProt: P0A988, DNA-directed DNA polymerase | ||
#3: Chemical | #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: 2.42 Å3/Da / Density % sol: 49.24 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100mM Na MES pH 6.0, 50-60mM CaCl2, 30%(v/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2007 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 57969 / Num. obs: 57969 / % possible obs: 94.8 % / Observed criterion σ(I): -4 / Rmerge(I) obs: 0.243 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 5356 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MMI Resolution: 1.9→24.69 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.885 / SU B: 5.339 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.483 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→24.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.896→1.945 Å / Total num. of bins used: 20
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