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- PDB-5y5c: Crystal structure of dha bind to bovine beta-lactoglobulin -

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Basic information

Entry
Database: PDB / ID: 5y5c
TitleCrystal structure of dha bind to bovine beta-lactoglobulin
ComponentsBeta-lactoglobulin
KeywordsLIPID BINDING PROTEIN / Lactoglobulin Fatty acid Crystal structure
Function / homology
Function and homology information


retinol binding / long-chain fatty acid binding / extracellular region / 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 beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsJiang, L. / Liu, J.
CitationJournal: To Be Published
Title: Crystal structure of dha bind to bovine beta-lactoglobulin
Authors: Jiang, L. / Liu, J.
History
DepositionAug 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactoglobulin
B: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2594
Polymers36,6022
Non-polymers6572
Water43224
1
A: Beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)18,3011
Polymers18,3011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-1 kcal/mol
Surface area8070 Å2
MethodPISA
2
B: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9583
Polymers18,3011
Non-polymers6572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-1 kcal/mol
Surface area7970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.490, 52.490, 108.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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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 (domestic cattle) / References: UniProt: P02754
#2: Chemical ChemComp-HXA / DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID


Mass: 328.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5 / Details: 1.34M trisodium citrate, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 11464 / % possible obs: 98.4 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 24

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GJ5

2gj5


Resolution: 2.61→45.46 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.89 / SU B: 10.918 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R Free: 0.336 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24389 477 4.8 %RANDOM
Rwork0.19992 ---
obs0.20207 9490 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.897 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å2-0 Å2
2--0.02 Å20 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.61→45.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 48 24 2531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192551
X-RAY DIFFRACTIONr_bond_other_d0.0030.022515
X-RAY DIFFRACTIONr_angle_refined_deg1.6512.0083442
X-RAY DIFFRACTIONr_angle_other_deg1.05435822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9885315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83626.36499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.61315468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.157156
X-RAY DIFFRACTIONr_chiral_restr0.0980.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212811
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02503
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.114.5311266
X-RAY DIFFRACTIONr_mcbond_other3.1034.531265
X-RAY DIFFRACTIONr_mcangle_it5.3536.7881579
X-RAY DIFFRACTIONr_mcangle_other5.3536.7891580
X-RAY DIFFRACTIONr_scbond_it2.8264.7831285
X-RAY DIFFRACTIONr_scbond_other2.8244.7851286
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8127.0081864
X-RAY DIFFRACTIONr_long_range_B_refined8.99234.8472646
X-RAY DIFFRACTIONr_long_range_B_other8.95534.8532644
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.607→2.675 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 45 -
Rwork0.21 679 -
obs--97.57 %

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