[English] 日本語
![](img/lk-miru.gif)
- PDB-2ftb: Crystal structure of axolotl (Ambystoma mexicanum) liver bile aci... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2ftb | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of axolotl (Ambystoma mexicanum) liver bile acid-binding protein bound to oleic acid | ||||||
![]() | Fatty acid-binding protein 2, liver | ||||||
![]() | LIPID BINDING PROTEIN / liver bile acid-binding protein / liver basic fatty acid-binding protein / axolotl / oleic acid / BABP / Lb-FABP | ||||||
Function / homology | ![]() | ||||||
Biological species | Ambystoma mexicanum (axolotl) | ||||||
Method | ![]() ![]() | ||||||
![]() | Capaldi, S. / Guariento, M. / Perduca, M. / Di Pietro, S.M. / Santome, J.A. / Monaco, H.L. | ||||||
![]() | ![]() Title: Crystal structure of axolotl (Ambystoma mexicanum) liver bile acid-binding protein bound to cholic and oleic acid Authors: Capaldi, S. / Guariento, M. / Perduca, M. / Di Pietro, S.M. / Santome, J.A. / Monaco, H.L. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystallization and preliminary X-ray study of two liver basic fatty acid-binding proteins Authors: Di Pietro, S.M. / Perduca, M. / Santome, J.A. / Monaco, H.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 37.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 25.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 677.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 678.4 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 9.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ft9C ![]() 1tvqS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 13758.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ambystoma mexicanum (axolotl) / Tissue: liver / References: UniProt: P81400 |
---|---|
#2: Chemical | ChemComp-OLA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.29 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 4000, 0.2M sodium acetate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 9, 2000 / Details: graphite crystal monochromator |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→45 Å / Num. all: 9823 / Num. obs: 9823 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.041 |
Reflection shell | Resolution: 2→2.05 Å / Rsym value: 0.185 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TVQ Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.95 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.801 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
|