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Open data
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Basic information
Entry | Database: PDB / ID: 1isq | ||||||
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Title | Pyrococcus furiosus PCNA complexed with RFCL PIP-box peptide | ||||||
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![]() | DNA BINDING PROTEIN / Toroidal trimer | ||||||
Function / homology | ![]() DNA clamp loader activity / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / translesion synthesis / DNA replication / DNA binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Matsumiya, S. / Ishino, S. / Ishino, Y. / Morikawa, K. | ||||||
![]() | ![]() Title: Physical interaction between proliferating cell nuclear antigen and replication factor C from Pyrococcus furiosus 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 | ![]() | 61.3 KB | Display | ![]() |
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PDB format | ![]() | 44.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.9 KB | Display | ![]() |
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Full document | ![]() | 444.5 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ge8S S: Starting model for refinement |
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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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Unit cell |
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Details | The second and third parts of the biological assembly are generated by the three-fold axis: -y, x-y, z and y-x+1, -x+1, z. |
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Components
#1: Protein | Mass: 28018.215 Da / Num. of mol.: 1 / Mutation: M73L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1367.654 Da / Num. of mol.: 1 / Fragment: C-terminal PIP-box region / Source method: obtained synthetically Details: This sequence corresponds to the residues 469-479 of Pyrococcus furiosus replication factor C large subunit. References: GenBank: 6539526, UniProt: Q9UWR2*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.71 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: ammonium sulfate, sodium citrate, glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 104 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Feb 17, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 13871 / Num. obs: 13871 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 41.01 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 19.32 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.24 / Num. unique all: 1377 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. obs: 13867 / Redundancy: 4.4 % / Num. measured all: 60038 / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 99.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1GE8 Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 38.192 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å
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Refinement | *PLUS Rfactor Rfree: 0.2913 / Rfactor Rwork: 0.2348 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.3119 / Rfactor Rwork: 0.2575 |