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- PDB-7n5l: PCNA from Thermococcus gammatolerans: crystal II, collection 20, ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7n5l | ||||||
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Title | PCNA from Thermococcus gammatolerans: crystal II, collection 20, 3.07 A, 77.0 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 | ![]() | 221.9 KB | Display | ![]() |
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PDB format | ![]() | 178.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496.6 KB | Display | ![]() |
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Full document | ![]() | 511.7 KB | Display | |
Data in XML | ![]() | 42.7 KB | Display | |
Data in CIF | ![]() | 58.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7n5iC ![]() 7n5jC ![]() 7n5kC ![]() 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: 2.7 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: 3.07→40.635 Å / Num. obs: 24414 / % possible obs: 99.7 % / Redundancy: 10.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.254 / Net I/σ(I): 12.45 |
Reflection shell | Resolution: 3.07→3.18 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.172 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 2386 / CC1/2: 0.768 / % possible all: 99.92 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5A6D Resolution: 3.07→40.635 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.05 / 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: 171.45 Å2 / Biso mean: 77.3854 Å2 / Biso min: 34.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.07→40.635 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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