[English] 日本語
![](img/lk-miru.gif)
- PDB-5vit: Crystal structure of a Pseudomonas malonate decarboxylase hetero-... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5vit | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer in complex with malonate | ||||||
![]() |
| ||||||
![]() | TRANSFERASE / acyl carrier protein / acetyl-CoA carboxylase | ||||||
Function / homology | ![]() malonyl-S-ACP:biotin-protein carboxyltransferase / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / carboxy-lyase activity / acyl carrier activity / fatty acid biosynthetic process / transferase activity / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maderbocus, R. / Tong, L. | ||||||
![]() | ![]() Title: Crystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer. Authors: Maderbocus, R. / Fields, B.L. / Hamilton, K. / Luo, S. / Tran, T.H. / Dietrich, L.E.P. / Tong, L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 912.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 740.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
5 | ![]()
| ||||||||
6 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 4 types, 16 molecules APIVCRKXDSLYETMZ
#1: Protein | Mass: 61501.242 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: mdcA, PA0208 / Production host: ![]() ![]() #2: Protein | Mass: 10692.981 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: mdcC, PFL_5818 / Production host: ![]() ![]() #3: Protein | Mass: 30371.320 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: madC, mdcD, AO964_31600, AOY09_06294, BH593_13640, PAERUG_E15_London_28_01_14_07061, PAERUG_P32_London_17_VIM_2_10_11_04127, PAMH19_0209 Production host: ![]() ![]() References: UniProt: A0A071KS24, UniProt: Q9I6S7*PLUS, malonyl-S-ACP:biotin-protein carboxyltransferase, methylmalonyl-CoA carboxytransferase #4: Protein | Mass: 30351.605 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: madD, AO964_31595, AOY09_06293, PAERUG_E15_London_28_01_14_07062, PAERUG_P32_London_17_VIM_2_10_11_04128 Production host: ![]() ![]() References: UniProt: A0A0C6EV56, UniProt: Q9I6S6*PLUS, malonyl-S-ACP:biotin-protein carboxyltransferase |
---|
-Non-polymers , 2 types, 1463 molecules ![](data/chem/img/MLI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-MLI / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.38 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% (w/v) PEG3350 and 8% Tacsimate / PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2015 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 294135 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 1.6 / % possible all: 95.3 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.203→49.043 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|