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Yorodumi- PDB-5dai: Proliferating cell nuclear antigen homolog 1 bound to FEN-1 peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dai | ||||||
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Title | Proliferating cell nuclear antigen homolog 1 bound to FEN-1 peptide | ||||||
Components |
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Keywords | TRANSFERASE / complex / PIP box binder | ||||||
Function / homology | Function and homology information 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / translesion synthesis / DNA replication / Hydrolases; Acting on ester bonds ...5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / translesion synthesis / DNA replication / Hydrolases; Acting on ester bonds / DNA repair / magnesium ion binding / DNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) Thermococcus kodakarensis KOD1 (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ladner, J.E. / Altieri, A.S. / Kelman, Z. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2016 Title: A small protein inhibits proliferating cell nuclear antigen by breaking the DNA clamp. Authors: Altieri, A.S. / Ladner, J.E. / Li, Z. / Robinson, H. / Sallman, Z.F. / Marino, J.P. / Kelman, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dai.cif.gz | 70.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dai.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 5dai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dai_validation.pdf.gz | 455.4 KB | Display | wwPDB validaton report |
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Full document | 5dai_full_validation.pdf.gz | 458.9 KB | Display | |
Data in XML | 5dai_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 5dai_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/5dai ftp://data.pdbj.org/pub/pdb/validation_reports/da/5dai | HTTPS FTP |
-Related structure data
Related structure data | 5da7C 3lx1S 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: 29099.311 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: pcn1, TK0535 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JF32 | ||
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#2: Protein/peptide | Mass: 1410.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermococcus kodakarensis KOD1 (archaea) / References: UniProt: Q5JGN0*PLUS | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.3 Details: Well solution: 2.8 M ammonium sulfate, 100 mM citric acid buffer pH 5.3, and 10% PEG 4000. Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→28.8 Å / Num. obs: 20143 / % possible obs: 98.2 % / Redundancy: 3.31 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 11.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LX1 Resolution: 2→28.762 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→28.762 Å
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Refine LS restraints |
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LS refinement shell |
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