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Open data
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Basic information
Entry | Database: PDB / ID: 5da7 | ||||||
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Title | monomeric PCNA bound to a small protein inhibitor | ||||||
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![]() | DNA binding protein/inhibitor / complex / inhibitor / DNA binding protein-inhibitor complex | ||||||
Function / homology | ![]() DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / DNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ladner, J.E. / Altieri, A.S. / Kelman, Z. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.8 KB | Display | ![]() |
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PDB format | ![]() | 99.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5daiC ![]() 3lx1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29099.311 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: pcn1, TK0535 / Production host: ![]() ![]() #2: Protein | Mass: 7629.947 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) ![]() ![]() References: UniProt: Q5JH72 #3: Chemical | ChemComp-SO4 / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.37 Å3/Da / Density % sol: 71.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: Well solution: 1.2 M ammonium sulfate, 50 mM sodium citrate buffer, and 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2014 |
Radiation | Monochromator: coated mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 30707 / % possible obs: 98.9 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 36.6 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.892 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LX1 Resolution: 2.802→29.962 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.15 / 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: 2.802→29.962 Å
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Refine LS restraints |
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LS refinement shell |
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