+
Open data
-
Basic information
Entry | Database: PDB / ID: 5tvo | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Trypanosoma brucei AdoMetDC-delta26 monomer | |||||||||
![]() | (S-adenosylmethionine decarboxylase proenzyme) x 2 | |||||||||
![]() | LYASE / autoinhibition / cis-proline | |||||||||
Function / homology | ![]() spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / putrescine binding / spermidine biosynthetic process / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Volkov, O.A. / Ariagno, C. / Chen, Z. / Tomchick, D.R. / Phillips, M.A. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Relief of autoinhibition by conformational switch explains enzyme activation by a catalytically dead paralog. Authors: Volkov, O.A. / Kinch, L.N. / Ariagno, C. / Deng, X. / Zhong, S. / Grishin, N.V. / Tomchick, D.R. / Chen, Z. / Phillips, M.A. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 201.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 161.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 447.5 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tvfC ![]() 5tvmC ![]() 3ep9S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 31971.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 927/4 GUTat10.1 / Gene: Tb927.6.4410, Tb927.6.4460 / Plasmid: pET28bSmt3 / Production host: ![]() ![]() References: UniProt: Q587A7, adenosylmethionine decarboxylase |
---|---|
#2: Protein | Mass: 6782.649 Da / Num. of mol.: 1 / Fragment: UNP residues 27-85 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 927/4 GUTat10.1 / Gene: Tb927.6.4410, Tb927.6.4460 / Production host: ![]() ![]() References: UniProt: Q587A7, adenosylmethionine decarboxylase |
#3: Chemical | ChemComp-PYR / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.45 % / Description: block |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25 % PEG 3350, 0.2 M Ammonium acetate, 0.1 M Bis-tris, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2015 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→50 Å / Num. obs: 51575 / % possible obs: 98.2 % / Redundancy: 9.4 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.048 / Net I/σ(I): 29.8 |
Reflection shell | Resolution: 1.48→1.51 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 4315 / CC1/2: 0.68 / % possible all: 79.2 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3EP9 Resolution: 1.481→38.006 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.28 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.481→38.006 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|