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Yorodumi- PDB-7q2p: Beta-lactoglobulin mutant FAW (I56F/L39A/M107W) in complex with d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q2p | ||||||
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Title | Beta-lactoglobulin mutant FAW (I56F/L39A/M107W) in complex with desipramine (FAW-DSM#2) | ||||||
Components | Beta-lactoglobulin | ||||||
Keywords | TRANSPORT PROTEIN / lactoglobulin / mutation / desipramine | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Loch, J.I. / Barciszewski, J. / Pokrywka, K. / Lewinski, K. | ||||||
Funding support | 1items
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Citation | Journal: Iucrj / Year: 2022 Title: New ligand-binding sites identified in the crystal structures of [beta]-lactoglobulin complexes with desipramine Authors: Loch, J.I. / Barciszewski, J. / Sliwiak, J. / Bonarek, P. / Wrobel, P. / Pokrywka, K. / Shabalin, I.G. / Minor, W. / Jaskolski, M. / Lewinski, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q2p.cif.gz | 135.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q2p.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7q2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q2p_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7q2p_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7q2p_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 7q2p_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/7q2p ftp://data.pdbj.org/pub/pdb/validation_reports/q2/7q2p | HTTPS FTP |
-Related structure data
Related structure data | 7q17C 7q18C 7q19C 7q2nC 7q2oC 1bsyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 9 - 162 / Label seq-ID: 9 - 162
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | Mass: 18279.965 Da / Num. of mol.: 2 / Mutation: L1A, I2S, L39A, I56F, M107W 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) / Strain (production host): Origami B (DE3) / References: UniProt: P02754 |
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-Non-polymers , 5 types, 177 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.40 M (NH4)2SO4, 0.5 M Tris-HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.688→45.519 Å / Num. obs: 39985 / % possible obs: 99.6 % / Redundancy: 12.94 % / CC1/2: 1 / Rrim(I) all: 0.072 / Net I/σ(I): 19.43 |
Reflection shell | Resolution: 1.69→1.79 Å / Num. unique obs: 6354 / CC1/2: 0.857 / Rrim(I) all: 1.68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BSY Resolution: 1.69→45.519 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 9.646 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.1 / ESU R Free: 0.106 / Details: Hydrogen atoms were added at riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.721 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→45.519 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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