[English] 日本語
![](img/lk-miru.gif)
- PDB-1iz4: Pyrococcus furiosus PCNA mutant (Met73Leu/Asp143Ala): tetragonal form -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1iz4 | ||||||
---|---|---|---|---|---|---|---|
Title | Pyrococcus furiosus PCNA mutant (Met73Leu/Asp143Ala): tetragonal 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 59 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 43.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 437.5 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1iz5C ![]() 1ge8S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 27974.205 Da / Num. of mol.: 1 / Mutation: M73L, D143A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.36 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: ammonium sulfate, sodium citrate, glycerol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 14, 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: 2→35 Å / Num. all: 22362 / Num. obs: 22310 / % possible obs: 95.9 % / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Biso Wilson estimate: 38.25 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.06 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3243 / Rsym value: 0.459 / % possible all: 97.4 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å / Num. measured all: 91731 |
Reflection shell | *PLUS % possible obs: 97.4 % |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1GE8 Resolution: 2→35 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.84 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→35 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.07 Å
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 35 Å / Num. reflection obs: 20084 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|