[English] 日本語
![](img/lk-miru.gif)
- PDB-6unz: Crystal structure of cytosolic fumarate hydratase from Leishmania... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6unz | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of cytosolic fumarate hydratase from Leishmania major | ||||||||||||
![]() | fumarate hydratase 2 | ||||||||||||
![]() | LYASE / fumarate hydratase / fumarase / Leishmania major / holo | ||||||||||||
Function / homology | ![]() fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / glycosome / ciliary plasm / generation of precursor metabolites and energy / 4 iron, 4 sulfur cluster binding / protein homodimerization activity / metal ion binding ...fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / glycosome / ciliary plasm / generation of precursor metabolites and energy / 4 iron, 4 sulfur cluster binding / protein homodimerization activity / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Feliciano, P.R. / Drennan, C.L. | ||||||||||||
Funding support | ![]() ![]()
| ||||||||||||
![]() | ![]() Title: Structural and Biochemical Investigations of the [4Fe-4S] Cluster-Containing Fumarate Hydratase fromLeishmania major. Authors: Feliciano, P.R. / Drennan, C.L. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 787.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 644.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 147.5 KB | Display | |
Data in CIF | ![]() | 199.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6uo0C ![]() 6uoiC ![]() 6uojC ![]() 6up9C ![]() 6upmC ![]() 6upoC ![]() 6uq8C ![]() 6uq9C ![]() 6uqbC ![]() 6uqlC ![]() 6uqmC ![]() 6uqnC ![]() 5l2rS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
4 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-
Components
#1: Protein | Mass: 66513.469 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Friedlin / Gene: FH2, LMJF_29_1960 / Production host: ![]() ![]() #2: Chemical | ChemComp-SF4 / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.7 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5 Details: 12% v/v PEG3350, 10 mM ammonium citrate tribasic, 16 mM sodium acetate trihydrate, 20 mM sodium formate, 6.4 mM ammonium tartrate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2012 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.5 |
Reflection | Resolution: 3.195→50 Å / Num. obs: 75134 / % possible obs: 90.4 % / Redundancy: 3 % / CC1/2: 0.334 / Net I/σ(I): 5 |
Reflection shell | Resolution: 3.2→3.26 Å / Num. unique obs: 75134 / CC1/2: 0.334 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 5L2R Resolution: 3.195→49.708 Å / Cross valid method: THROUGHOUT / σ(F): 688.99 / Phase error: 29.79
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.75 Å2 / Biso mean: 63.242 Å2 / Biso min: 15.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.195→49.708 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
|