[English] 日本語
![](img/lk-miru.gif)
- PDB-5d2f: 4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - apo form -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5d2f | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | 4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - apo form | |||||||||||||||
![]() | 4-oxalocrotonate decarboxylase NahK | |||||||||||||||
![]() | LYASE / naphthalene degradation | |||||||||||||||
Function / homology | ![]() | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Guimaraes, S.L. / Nagem, R.A.P. | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() Title: Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous beta-Keto Acid. Authors: Guimaraes, S.L. / Coitinho, J.B. / Costa, D.M. / Araujo, S.S. / Whitman, C.P. / Nagem, R.A. | |||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 126.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 94.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 453.1 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 25.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5d2gC ![]() 5d2hC ![]() 5d2iC ![]() 5d2jC ![]() 5d2kC ![]() 2eb4S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 30746.088 Da / Num. of mol.: 1 / Mutation: L155P Source method: isolated from a genetically manipulated source Details: from plasmid NAH7 / Source: (gene. exp.) ![]() Details (production host): The thrombin site in the original pET28a vector was replaced by the TEV site for tag cleavage Production host: ![]() ![]() References: UniProt: Q1XGK3, 2-oxo-3-hexenedioate decarboxylase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.6 % / Description: parallelepiped-shaped |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: lithium sulfate monohydrate / PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.437 Å / Relative weight: 1 |
Reflection | Resolution: 1.7378→31.3577 Å / Num. obs: 25510 / % possible obs: 97.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 15.42 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.237 |
Reflection shell | Resolution: 1.7378→1.78 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 2.82 / % possible all: 94.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2EB4 Resolution: 1.738→31.353 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.8 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.49 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.738→31.353 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|