[English] 日本語
![](img/lk-miru.gif)
- PDB-1z33: Crystal structure of Trichomonas vaginalis purine nucleoside phos... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1z33 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Trichomonas vaginalis purine nucleoside phosphorylase | ||||||
![]() | purine nucleoside phosphorylase | ||||||
![]() | TRANSFERASE / alpha-beta-alpha sandwich | ||||||
Function / homology | Nucleoside phosphorylase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y. / Wang, W.H. / Wu, S.W. / Wang, C.C. / Ealick, S.E. | ||||||
![]() | ![]() Title: Identification of a subversive substrate of Trichomonas vaginalis purine nucleoside phosphorylase and the crystal structure of the enzyme-substrate complex. Authors: Zang, Y. / Wang, W.H. / Wu, S.W. / Ealick, S.E. / Wang, C.C. | ||||||
History |
| ||||||
Remark 999 | Sequence There is currently no match for the protein sequence in the standard databases |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 58.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 42.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 430.5 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1z34C ![]() 1z35C ![]() 1z36C ![]() 1z37C ![]() 1z38C ![]() 1z39C ![]() 1pkeS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| x 6|||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 25813.658 Da / Num. of mol.: 1 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: 4.3 Å3/Da / Density % sol: 70 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG400, ethylene glycol, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
---|---|
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→41.25 Å / Num. all: 12529 / Num. obs: 11760 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34 Å2 |
Reflection shell | Resolution: 2.7→2.87 Å / % possible all: 88.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1PKE Resolution: 2.7→41.25 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 270231.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.3946 Å2 / ksol: 0.372153 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→41.25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|