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Yorodumi- PDB-1j54: Structure of the N-terminal exonuclease domain of the epsilon sub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j54 | ||||||
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Title | Structure of the N-terminal exonuclease domain of the epsilon subunit of E.coli DNA polymerase III at pH 5.8 | ||||||
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: 1.7 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 | 1j54.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j54.ent.gz | 38.8 KB | Display | PDB format |
PDBx/mmJSON format | 1j54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/1j54 ftp://data.pdbj.org/pub/pdb/validation_reports/j5/1j54 | 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 on special symmetry positions |
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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 | ChemComp-TMP / | #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: 5.8 Details: PEG 8000, magnesium sulfate, cacodylate, pH 5.8, 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: 1.7→50 Å / Num. obs: 22532 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.8 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.152 / Num. unique all: 1813 / % possible all: 78 |
Reflection | *PLUS Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS Rmerge(I) obs: 0.152 |
-Processing
Software |
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Refinement | Resolution: 1.7→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)
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree: 0.234 / Rfactor Rwork: 0.201 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |