[English] 日本語
![](img/lk-miru.gif)
- PDB-6vin: Crystallographic structure of the circularly permuted human Taspa... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6vin | ||||||
---|---|---|---|---|---|---|---|
Title | Crystallographic structure of the circularly permuted human Taspase1 protein | ||||||
![]() | Threonine aspartase 1 | ||||||
![]() | HYDROLASE / Taspase1 / enzyme / asparaginase / X-ray structure. | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Threonine endopeptidases / asparaginase activity / Formation of WDR5-containing histone-modifying complexes / beta-aspartyl-peptidase activity / protein maturation / threonine-type endopeptidase activity / epigenetic regulation of gene expression / positive regulation of DNA-templated transcription / proteolysis / identical protein binding ...Hydrolases; Acting on peptide bonds (peptidases); Threonine endopeptidases / asparaginase activity / Formation of WDR5-containing histone-modifying complexes / beta-aspartyl-peptidase activity / protein maturation / threonine-type endopeptidase activity / epigenetic regulation of gene expression / positive regulation of DNA-templated transcription / proteolysis / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Martin-Garcia, J.M. / Fromme, P. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural insights into the function of the catalytically active human Taspase1. Authors: Nagaratnam, N. / Delker, S.L. / Jernigan, R. / Edwards, T.E. / Snider, J. / Thifault, D. / Williams, D. / Nannenga, B.L. / Stofega, M. / Sambucetti, L. / Hsieh, J.J. / Flint, A.J. / Fromme, ...Authors: Nagaratnam, N. / Delker, S.L. / Jernigan, R. / Edwards, T.E. / Snider, J. / Thifault, D. / Williams, D. / Nannenga, B.L. / Stofega, M. / Sambucetti, L. / Hsieh, J.J. / Flint, A.J. / Fromme, P. / Martin-Garcia, J.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 248.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 206.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 250 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 250 KB | Display | |
Data in XML | ![]() | 1.5 KB | Display | |
Data in CIF | ![]() | 8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ugkSC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 41239.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9H6P5, Hydrolases; Acting on peptide bonds (peptidases); Threonine endopeptidases |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.3 Å3/Da / Density % sol: 70 % Description: Cuboids of size range between 200 and 500 microns |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 0.1 M sodium citrate pH 4.0, 1.0 M ammonium sulfate, 10% 2-methyl-2,4-pentanediol (MPD), and 0.4 M NaCl PH range: 4.0-4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.04→49.05 Å / Num. obs: 15315 / % possible obs: 93.9 % / Redundancy: 19.6 % / CC1/2: 1 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 3.04→3.11 Å / Rmerge(I) obs: 1.8 / Num. unique obs: 15315 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6UGK Resolution: 3.04→49.05 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.74 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 462.8 Å2 / Biso mean: 152.987 Å2 / Biso min: 0.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.04→49.05 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.04→3.116 Å / Rfactor Rfree error: 0
|