[English] 日本語
Yorodumi- PDB-6rwp: Engineered beta-lactoglobulin: variant L58F in complex with myris... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rwp | ||||||
---|---|---|---|---|---|---|---|
Title | Engineered beta-lactoglobulin: variant L58F in complex with myristic acid | ||||||
Components | Beta-lactoglobulin | ||||||
Keywords | TRANSPORT PROTEIN / Lipocalin / mutation / lactoglobulin | ||||||
Function / homology | Function and homology information retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Loch, J.I. / Kaczor, K. / Lewinski, K. | ||||||
Funding support | Poland, 1items
| ||||||
Citation | Journal: J.Struct.Biol. / Year: 2020 Title: Structure-based design approach to rational site-directed mutagenesis of beta-lactoglobulin. Authors: Bonarek, P. / Loch, J.I. / Tworzydlo, M. / Cooper, D.R. / Milto, K. / Wrobel, P. / Kurpiewska, K. / Lewinski, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6rwp.cif.gz | 76.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6rwp.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 6rwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/6rwp ftp://data.pdbj.org/pub/pdb/validation_reports/rw/6rwp | HTTPS FTP |
---|
-Related structure data
Related structure data | 6qi6C 6qi7C 6qpdC 6qpeC 6rwqC 6rwrC 6rytC 6xveC 1bsyS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18267.031 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L58F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: LGB / Plasmid: pET-Duet-1 / Production host: Escherichia coli (E. coli) / Variant (production host): Origami B (DE3) / References: UniProt: P02754 |
---|---|
#2: Chemical | ChemComp-MYR / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.38 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2.80 M (NH4)2SO4 in 0.1 M Tris-HCl pH 8.0, 5 mM myristic acid |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Nov 14, 2014 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→15.18 Å / Num. obs: 11062 / % possible obs: 99.3 % / Redundancy: 2.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.04 / Rrim(I) all: 0.072 / Net I/σ(I): 10.6 / Num. measured all: 31724 / Scaling rejects: 32 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BSY Resolution: 2.1→14.78 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.12 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.19 / 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: 29.32 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→14.78 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|