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- PDB-7kp5: Energetic and structural effects of the Tanford transition on the... -

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Basic information

Entry
Database: PDB / ID: 7kp5
TitleEnergetic and structural effects of the Tanford transition on the ligand recognition of bovine Beta-lactoglobulin
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT 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
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin signature.
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRodriguez-Hernandez, A. / Rodriguez-Romero, A.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)235831 Mexico
CitationJournal: 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
DepositionNov 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA1: Beta-lactoglobulin
BA1: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4025
Polymers36,6022
Non-polymers7993
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.747, 69.788, 140.331
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Beta-lactoglobulin / / Beta-LG


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 ChemComp-SDS / DODECYL SULFATE / Sodium dodecyl sulfate


Mass: 266.397 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.39→2.43 Å / Num. unique obs: 697 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BEB

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
RfactorNum. reflection% reflection
Rfree0.2685 994 6.91 %
Rwork0.2347 13394 -
obs0.237 14388 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.76 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 51 35 2385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422389
X-RAY DIFFRACTIONf_angle_d0.75833262
X-RAY DIFFRACTIONf_chiral_restr0.0483395
X-RAY DIFFRACTIONf_plane_restr0.0042417
X-RAY DIFFRACTIONf_dihedral_angle_d7.41371454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.520.31921370.31171829X-RAY DIFFRACTION97.91
2.52-2.680.3161400.28021891X-RAY DIFFRACTION99.95
2.68-2.890.38721400.28251880X-RAY DIFFRACTION99.85
2.89-3.180.30341400.27531890X-RAY DIFFRACTION99.51
3.18-3.640.25561430.22031924X-RAY DIFFRACTION99.95
3.64-4.580.22851410.2051924X-RAY DIFFRACTION98.71
4.58-38.860.25511530.2262056X-RAY DIFFRACTION99.64

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