+Open data
-Basic information
Entry | Database: PDB / ID: 8djq | ||||||
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Title | Sliding-clamp-DnaE1 peptide | ||||||
Components |
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Keywords | DNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information DNA polymerase III complex / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycolicibacterium thermoresistibile ATCC 19527 (bacteria) Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Kapur, M.K. / Gray, O.J. / Honzatko, R.H. / Nelson, S.N. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Interaction of the sliding clamp with mycobacterial polymerases Authors: Kapur, M.K. / Gray, O.J. / Honzatko, R.H. / Nelson, S.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8djq.cif.gz | 662.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8djq.ent.gz | 466.7 KB | Display | PDB format |
PDBx/mmJSON format | 8djq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/8djq ftp://data.pdbj.org/pub/pdb/validation_reports/dj/8djq | HTTPS FTP |
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-Related structure data
Related structure data | 8dj6S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41677.191 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium thermoresistibile ATCC 19527 (bacteria) Strain: ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316 Gene: KEK_10778 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / References: UniProt: G7CIP4 #2: Protein/peptide | Mass: 725.789 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria) / References: UniProt: P63978, DNA-directed DNA polymerase #3: Chemical | ChemComp-ACE / #4: Chemical | ChemComp-NH2 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.45 Å3/Da / Density % sol: 49.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.5M Ammonium sulphate, 0.1 M sodium acetate tribasic pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.062 Å / Num. obs: 38932 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 60.4 Å2 / CC1/2: 0.967 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.098 / Net I/σ(I): 4.75 |
Reflection shell | Resolution: 2.8→2.85 Å / Num. unique obs: 1673 / CC1/2: 0.967 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8DJ6 Resolution: 2.8→19.87 Å / SU ML: 0.5943 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.0642 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→19.87 Å
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Refine LS restraints |
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LS refinement shell |
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