[English] 日本語
![](img/lk-miru.gif)
- PDB-1iqp: Crystal Structure of the Clamp Loader Small Subunit from Pyrococc... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1iqp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus | ||||||
![]() | RFCS | ||||||
![]() | REPLICATION / CLAMP LOADER / EXTENDED AAA-ATPASE DOMAIN / COMPLEX WITH ADP | ||||||
Function / homology | ![]() four-way junction helicase activity / intein-mediated protein splicing / endonuclease activity / DNA recombination / DNA replication / DNA repair / DNA binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oyama, T. / Ishino, Y. / Cann, I.K.O. / Ishino, S. / Morikawa, K. | ||||||
![]() | ![]() Title: Atomic Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus Authors: Oyama, T. / Ishino, Y. / Cann, I.K.O. / Ishino, S. / Morikawa, K. #1: ![]() Title: Biochemical analysis of replication factor C from the hyperthermophilic archaeon Pyrococcus furiosus Authors: Cann, I.K.O. / Ishino, S. / Yuasa, M. / Daiyasu, H. / Toh, H. / Ishino, Y. #2: ![]() Title: Three-dimensional electron microscopy of the clamp loader small subunit from Pyrococcus furiosus Authors: Mayanagi, K. / Miyata, T. / Oyama, T. / Ishino, Y. / Morikawa, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 389.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 322.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 79.9 KB | Display | |
Data in CIF | ![]() | 107.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 37458.531 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ADP / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: MPD, glycerol, sodium chloride, acetic acid, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jul 8, 1999 / Details: mirros |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→65 Å / Num. all: 80855 / Num. obs: 76556 / % possible obs: 93.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.037 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 4.5 / Num. unique all: 6221 / % possible all: 78.7 |
Reflection | *PLUS Lowest resolution: 65 Å / Num. measured all: 260398 |
Reflection shell | *PLUS % possible obs: 78.7 % |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 15 Å / σ(F): 1 / % reflection Rfree: 5.35 % / Rfactor obs: 0.224 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.16 |