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Yorodumi- PDB-7kp5: Energetic and structural effects of the Tanford transition on the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kp5 | ||||||
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Title | Energetic and structural effects of the Tanford transition on the ligand recognition of bovine Beta-lactoglobulin | ||||||
Components | Beta-lactoglobulin | ||||||
Keywords | TRANSPORT PROTEIN / Bovine beta-lactoglobulin / Lipocalin / Tanford transition / Structural energetics | ||||||
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: 2.4 Å | ||||||
Authors | Rodriguez-Hernandez, A. / Rodriguez-Romero, A. | ||||||
Funding support | Mexico, 1items
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Citation | Journal: Arch.Biochem.Biophys. / Year: 2021 Title: Energetic and structural effects of the Tanford transition on ligand recognition of bovine beta-lactoglobulin. Authors: Labra-Nunez, A. / Cofas-Vargas, L.F. / Gutierrez-Magdaleno, G. / Gomez-Velasco, H. / Rodriguez-Hernandez, A. / Rodriguez-Romero, A. / Garcia-Hernandez, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kp5.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kp5.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7kp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kp5_validation.pdf.gz | 900.6 KB | Display | wwPDB validaton report |
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Full document | 7kp5_full_validation.pdf.gz | 939.8 KB | Display | |
Data in XML | 7kp5_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 7kp5_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/7kp5 ftp://data.pdbj.org/pub/pdb/validation_reports/kp/7kp5 | HTTPS FTP |
-Related structure data
Related structure data | 7kotC 1bebS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18301.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02754 #2: Chemical | #3: Water | ChemComp-HOH / | 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: 2.39 Å3/Da / Density % sol: 48.56 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 12-15 mg/mL protein in 0.05M acetate and 0.1 M NaCl. Combined 1:1 with 0.05M KH2PO4, 20% PEG |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→38.86 Å / Num. obs: 14623 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 49.5 Å2 / CC1/2: 0.95 / Net I/σ(I): 35.7 |
Reflection shell | Resolution: 2.39→2.43 Å / Num. unique obs: 697 / CC1/2: 0.85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BEB Resolution: 2.4→38.86 Å / SU ML: 0.2816 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6508 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.76 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→38.86 Å
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Refine LS restraints |
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LS refinement shell |
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