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- PDB-1iz5: Pyrococcus furiosus PCNA mutant (Met73Leu, Asp143Ala, Asp147Ala):... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1iz5 | ||||||
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Title | Pyrococcus furiosus PCNA mutant (Met73Leu, Asp143Ala, Asp147Ala): orthorhombic form | ||||||
![]() | Proliferating cell nuclear antigen | ||||||
![]() | DNA BINDING PROTEIN / DNA / REPLICATION / PROCESSIVITY / SLIDING CLAMP | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Matsumiya, S. / Ishino, S. / Ishino, Y. / Morikawa, K. | ||||||
![]() | ![]() Title: Intermolecular ion pairs maintain the toroidal structure of Pyrococcus furiosus PCNA Authors: Matsumiya, S. / Ishino, S. / Ishino, Y. / Morikawa, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.7 KB | Display | ![]() |
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PDB format | ![]() | 82.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.2 KB | Display | ![]() |
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Full document | ![]() | 446.3 KB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1iz4C ![]() 1ge8S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27930.195 Da / Num. of mol.: 2 / Mutation: M73L, D143A, D147A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 57.99 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: ammonium sulfate, 2-methyl-2,4-pentanediol, sodium citrate, glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 13, 2001 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.836 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→35 Å / Num. all: 60694 / Num. obs: 60694 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 33.78 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.073 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 1.4 / Num. unique all: 8697 / Rsym value: 0.5 / % possible all: 98.8 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 214024 |
Reflection shell | *PLUS % possible obs: 98.8 % / Redundancy: 6.2 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1GE8 Resolution: 1.8→35 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 33.3044 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å
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Refinement | *PLUS Num. reflection obs: 54547 / Rfactor Rfree: 0.2975 / Rfactor Rwork: 0.2715 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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