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Yorodumi- PDB-6izo: Crystal structure of DNA polymerase sliding clamp from Caulobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6izo | |||||||||
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Title | Crystal structure of DNA polymerase sliding clamp from Caulobacter crescentus | |||||||||
Components | Beta sliding clamp | |||||||||
Keywords | TRANSFERASE / DNA BINDING PROTEIN / PROTEIN BINDING / Homodimer | |||||||||
Function / homology | Function and homology information DNA polymerase III complex / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Caulobacter vibrioides CB15 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | |||||||||
Authors | Jiang, X. / Zhang, L. / Teng, M. / Li, X. | |||||||||
Funding support | China, 2items
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Citation | Journal: Febs J. / Year: 2020 Title: Caulobacter crescentus beta sliding clamp employs a noncanonical regulatory model of DNA replication. Authors: Jiang, X. / Zhang, L. / An, J. / Wang, M. / Teng, M. / Guo, Q. / Li, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6izo.cif.gz | 154 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6izo.ent.gz | 118.5 KB | Display | PDB format |
PDBx/mmJSON format | 6izo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/6izo ftp://data.pdbj.org/pub/pdb/validation_reports/iz/6izo | HTTPS FTP |
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-Related structure data
Related structure data | 6jirC 4tr8S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42559.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides CB15 (bacteria) / Gene: dnaN, CC_0156 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P0CAU5 #2: Chemical | #3: Chemical | ChemComp-PEG / | #4: 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: 2.59 Å3/Da / Density % sol: 52.47 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 10% PEG2000, 0.1M calcium acetate, 0.1M Na acetate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. obs: 63559 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.5 Å2 / Rpim(I) all: 0.04 / Rrim(I) all: 0.074 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.94→2.03 Å / Mean I/σ(I) obs: 4.38 / Num. unique obs: 3421 / CC1/2: 0.969 / Rpim(I) all: 0.138 / Rrim(I) all: 0.264 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TR8 Resolution: 1.94→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.216 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.133 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.112 Å2
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Refinement step | Cycle: 1 / Resolution: 1.94→50 Å
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Refine LS restraints |
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