+Open data
-Basic information
Entry | Database: PDB / ID: 4gx8 | ||||||
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Title | Crystal structure of a DNA polymerase III alpha-epsilon chimera | ||||||
Components | DNA polymerase III subunit epsilon,DNA polymerase III subunit alpha | ||||||
Keywords | TRANSFERASE / DNA polymerase III / polIII epsilon / polIII alpha / DnaQ / DnaE | ||||||
Function / homology | Function and homology information DNA polymerase III, core complex / DNA polymerase III complex / lagging strand elongation / replisome / exonuclease activity / DNA replication proofreading / leading strand elongation / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase ...DNA polymerase III, core complex / DNA polymerase III complex / lagging strand elongation / replisome / exonuclease activity / DNA replication proofreading / leading strand elongation / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Robinson, A. / Horan, N. / Xu, Z.-Q. / Dixon, N.E. / Oakley, A.J. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2013 Title: Proofreading exonuclease on a tether: the complex between the E. coli DNA polymerase III subunits alpha, {varepsilon}, theta and beta reveals a highly flexible arrangement of the proofreading domain Authors: Ozawa, K. / Horan, N.P. / Robinson, A. / Yagi, H. / Hill, F.R. / Jergic, S. / Xu, Z.Q. / Loscha, K.V. / Li, N. / Tehei, M. / Oakley, A.J. / Otting, G. / Huber, T. / Dixon, N.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gx8.cif.gz | 275.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gx8.ent.gz | 223.8 KB | Display | PDB format |
PDBx/mmJSON format | 4gx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gx8_validation.pdf.gz | 457.8 KB | Display | wwPDB validaton report |
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Full document | 4gx8_full_validation.pdf.gz | 466.4 KB | Display | |
Data in XML | 4gx8_validation.xml.gz | 54.8 KB | Display | |
Data in CIF | 4gx8_validation.cif.gz | 82.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/4gx8 ftp://data.pdbj.org/pub/pdb/validation_reports/gx/4gx8 | HTTPS FTP |
-Related structure data
Related structure data | 4gx9C 2hnhS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 6
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-Components
#1: Protein | Mass: 34628.246 Da / Num. of mol.: 4 Fragment: polIII epsilon C-terminal domain (UNP residues 209-243),polIII alpha PHP domain (UNP residues 1-270) Mutation: L66P,L66P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dnaQ, mutD, b0215, JW0205, dnaE, polC, b0184, JW0179 / Plasmid: pETMCS1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 P lysS References: UniProt: P03007, UniProt: P10443, DNA-directed DNA polymerase #2: Chemical | ChemComp-CL / #3: 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: 2.38 Å3/Da / Density % sol: 48.29 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.96858 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 1, 2010 / Details: beamline optics |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96858 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→23.24 Å / Num. all: 140494 / Num. obs: 140494 / % possible obs: 98.1 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 7 % / Biso Wilson estimate: 16.704 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 3.7 / Num. unique all: 20221 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HNH Resolution: 1.7→23.04 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.667 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): -1 / ESU R: 0.13 / ESU R Free: 0.123 / 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: 18.958 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→23.04 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 2148 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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