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Yorodumi- PDB-1j53: Structure of the N-terminal Exonuclease Domain of the Epsilon Sub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j53 | ||||||
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Title | Structure of the N-terminal Exonuclease Domain of the Epsilon Subunit of E.coli DNA Polymerase III at pH 8.5 | ||||||
Components | DNA polymerase III, epsilon chain | ||||||
Keywords | TRANSFERASE / DNA polymerase proofreading domain | ||||||
Function / homology | Function and homology information DNA polymerase III, core complex / DNA replication proofreading / DNA polymerase III complex / lagging strand elongation / replisome / exonuclease activity / leading strand elongation / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase ...DNA polymerase III, core complex / DNA replication proofreading / DNA polymerase III complex / lagging strand elongation / replisome / exonuclease activity / 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 / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Hamdan, S. / Carr, P.D. / Brown, S.E. / Ollis, D.L. / Dixon, N.E. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Structural Basis for Proofreading during Replication of the Escherichia coli Chromosome Authors: Hamdan, S. / Carr, P.D. / Brown, S.E. / Ollis, D.L. / 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 | 1j53.cif.gz | 54.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j53.ent.gz | 39.1 KB | Display | PDB format |
PDBx/mmJSON format | 1j53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/1j53 ftp://data.pdbj.org/pub/pdb/validation_reports/j5/1j53 | HTTPS FTP |
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-Related 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: 20741.689 Da / Num. of mol.: 1 / Fragment: N-terminal exonuclease domain (residues 1-186) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PSHSH1018 / Genus (production host): T7-like viruses / Production host: Enterobacteria phage T7 (virus) / References: UniProt: P03007, DNA-directed DNA polymerase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.47 Å3/Da / Density % sol: 50.29 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, magnesium sulfate, cacodylate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Details: Hamdan, S., (2000) J.Struct.Biol., 131, 164. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ESRF / Beamline: BM30A / Wavelength: 0.9796 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 5, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 20091 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.1 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.204 / Num. unique all: 1920 / % possible all: 98.4 |
Reflection | *PLUS Rmerge(I) obs: 0.041 |
Reflection shell | *PLUS Rmerge(I) obs: 0.204 |
-Processing
Software |
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Refinement | Resolution: 1.8→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: maximum likelihood target refinements (positional, individual B-factor, and simulated annealing using standard CNS scripts). The TMP 2100 molecule was fitted into the electron density but ...Details: maximum likelihood target refinements (positional, individual B-factor, and simulated annealing using standard CNS scripts). The TMP 2100 molecule was fitted into the electron density but not refined (as attempts to do so increased the Rfree value). The occupancies are zero.
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree: 0.227 / Rfactor Rwork: 0.199 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |