[English] 日本語
Yorodumi- PDB-4iba: Bovine beta-lactoglobulin (isoform B) in complex with dodecyl sul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iba | ||||||
---|---|---|---|---|---|---|---|
Title | Bovine beta-lactoglobulin (isoform B) in complex with dodecyl sulphate (SDS) | ||||||
Components | beta-lactoglobulin | ||||||
Keywords | TRANSPORT PROTEIN / lipocalin | ||||||
Function / homology | Function and homology information retinol binding / long-chain fatty acid binding / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Loch, J.I. / Bonarek, P. / Polit, A. / Swiatek, S. / Dziedzicka-Wasylewska, M. / Lewinski, K. | ||||||
Citation | Journal: J.Mol.Recognit. / Year: 2013 Title: The differences in binding 12-carbon aliphatic ligands by bovine beta-lactoglobulin isoform A and B studied by isothermal titration calorimetry and X-ray crystallography Authors: Loch, J.I. / Bonarek, P. / Polit, A. / Swiatek, S. / Dziedzicka-Wasylewska, M. / Lewinski, K. | ||||||
History |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4iba.cif.gz | 46.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4iba.ent.gz | 32.1 KB | Display | PDB format |
PDBx/mmJSON format | 4iba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iba_validation.pdf.gz | 613 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4iba_full_validation.pdf.gz | 615.4 KB | Display | |
Data in XML | 4iba_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 4iba_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/4iba ftp://data.pdbj.org/pub/pdb/validation_reports/ib/4iba | HTTPS FTP |
-Related structure data
Related structure data | 4ib6C 4ib7C 4ib8C 4ib9C 1bsyS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18301.174 Da / Num. of mol.: 1 / Fragment: UNP residues 17-178 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02754 |
---|---|
#2: Chemical | ChemComp-SDS / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.34M TRISODIUM CITRATE, 0.1M TRIS-HCL BUFFER, PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SEALED TUBE / Type: OTHER / Wavelength: 1.54 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Apr 24, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→12.99 Å / Num. all: 8639 / Num. obs: 8561 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.026 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 6.4 / Num. unique all: 1217 / % possible all: 98.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BSY Resolution: 2.3→12.99 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.901 / SU B: 8.618 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.395 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| |||||||||||||||||||||||||||||||||||||||||||||
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: 31.622 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→12.99 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.302→2.359 Å / Total num. of bins used: 20
|