[English] 日本語
![](img/lk-miru.gif)
- PDB-4gkp: Structure of the truncated neck and C-terminal motor homology dom... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4gkp | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the truncated neck and C-terminal motor homology domain of ViK1 from Candida glabrata | ||||||
![]() | Spindle pole body-associated protein VIK1 | ||||||
![]() | STRUCTURAL PROTEIN / kinesin motor domain-like fold / Microtubule binding protein / Kinesin associated protein / Kar3 | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Duan, D. / Allingham, J.S. | ||||||
![]() | ![]() Title: Neck Rotation and Neck Mimic Docking in the Noncatalytic Kar3-associated Protein Vik1. Authors: Duan, D. / Jia, Z. / Joshi, M. / Brunton, J. / Chan, M. / Drew, D. / Davis, D. / Allingham, J.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 108.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 81.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 442.5 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 25.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gkqC ![]() 4gkrC ![]() 2o0aS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 31902.449 Da / Num. of mol.: 2 / Fragment: UNP residues 313-584 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65 Gene: CAGL0D00638G, CAGL0H00638g / Plasmid: Modified pET16b / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.83 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, 13% PEG-6000, 5% isopropanol, 75mM NaAcetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 5, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.42→20 Å / Num. all: 22019 / Num. obs: 21752 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 49.904 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 37.65 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 2O0A Resolution: 2.42→19.83 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2543 / WRfactor Rwork: 0.2074 / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.8162 / SU B: 7.793 / SU ML: 0.184 / SU R Cruickshank DPI: 0.4339 / SU Rfree: 0.2752 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.434 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.62 Å2 / Biso mean: 43.2617 Å2 / Biso min: 17.4 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.42→19.83 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.42→2.482 Å / Total num. of bins used: 20
|