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- PDB-7n5j: PCNA from Thermococcus gammatolerans: crystal I, collection 5, 2.... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7n5j | ||||||
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Title | PCNA from Thermococcus gammatolerans: crystal I, collection 5, 2.82 A, 89.1 MGy | ||||||
![]() | DNA polymerase sliding clamp | ||||||
![]() | DNA BINDING PROTEIN / PCNA / sliding clamp / radioresistance / radiation damage / ionizing radiation | ||||||
Function / homology | ![]() DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / translesion synthesis / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Marin-Tovar, Y. / Rudino-Pinera, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: PCNA from Thermococcus gammatolerans: A protein involved in chromosomal DNA metabolism intrinsically resistant at high levels of ionizing radiation. Authors: Marin-Tovar, Y. / Serrano-Posada, H. / Diaz-Vilchis, A. / Rudino-Pinera, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 221.4 KB | Display | ![]() |
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PDB format | ![]() | 178 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7n5iC ![]() 7n5kC ![]() 7n5lC ![]() 7n5mC ![]() 7n5nC ![]() 5a6dS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 30191.521 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: DSM 15229 / JCM 11827 / EJ3 / Gene: pcn, TGAM_1046 / Plasmid: pCold-I / Production host: ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 5.2 Details: 100 mM sodium citrate pH 5.2, 3.2 M ammonium sulfate, 7.5% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.82→37.33 Å / Num. obs: 31591 / % possible obs: 99.75 % / Redundancy: 10.3 % / CC1/2: 0.979 / Rmerge(I) obs: 0.1524 / Net I/σ(I): 18.68 |
Reflection shell | Resolution: 2.82→2.92 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.205 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 3147 / CC1/2: 0.797 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5A6D Resolution: 2.82→37.326 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.04 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 161.64 Å2 / Biso mean: 72.9233 Å2 / Biso min: 36.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.82→37.326 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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