[English] 日本語
![](img/lk-miru.gif)
- PDB-6j57: Crystal structure of fumarylpyruvate hydrolase from Corynebacteri... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6j57 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of fumarylpyruvate hydrolase from Corynebacterium glutamicum | ||||||
![]() | Predicted 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() Lyases; Carbon-carbon lyases; Carboxy-lyases / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / catalytic activity / isomerase activity / lyase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hong, H. / Seo, H. / Kim, K.-J. / Park, W. | ||||||
![]() | ![]() Title: Sequence, structure and function-based classification of the broadly conserved FAH superfamily reveals two distinct fumarylpyruvate hydrolase subfamilies. Authors: Hong, H. / Seo, H. / Park, W. / Kim, K.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 124.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 97.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 478.5 KB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6j5xC ![]() 6j5yC ![]() 3rr6S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 31659.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.69 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Ammonium sulfate, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 4, 2016 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2→61.72 Å / Num. obs: 38656 / % possible obs: 98.5 % / Redundancy: 3.4 % / Rpim(I) all: 0.057 / Net I/σ(I): 19.04 |
Reflection shell | Resolution: 2→2.03 Å / Num. unique obs: 1864 / Rpim(I) all: 0.203 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3RR6 Resolution: 2.01→28.03 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.007 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.158 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: 86.75 Å2 / Biso mean: 22.14 Å2 / Biso min: 10.68 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.01→28.03 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.006→2.058 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|