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- PDB-9i7o: Beta-lactoglobulin complex with retinol -

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Basic information

Entry
Database: PDB / ID: 9i7o
TitleBeta-lactoglobulin complex with retinol
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / Complex / Retinol
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 / Lipocalin signature.
Similarity search - Domain/homology
RETINOL / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFigueiredo, M.R.F. / Pereira, P.J.B. / Martins, P.M.M.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia2023.00318.BD Portugal
CitationJournal: Food Chem / Year: 2026
Title: New solid formulations of retinol protected at the molecular level by the whey protein beta-lactoglobulin.
Authors: Figueiredo, M. / Sarkany, Z. / Pereira, P.J.B. / Rocha, F. / Martins, P.M.
History
DepositionJan 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2772
Polymers19,9901
Non-polymers2861
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.907, 53.907, 112.579
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 19990.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02754
#2: Chemical ChemComp-RTL / RETINOL


Mass: 286.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 47.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 2.4 M ammonium sulfate 0.5 M TRIS

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION GEMINI / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jun 18, 2024
RadiationMonochromator: Confocal Max-FluxTM optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→14.62 Å / Num. obs: 13345 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.034 / Rrim(I) all: 0.092 / Net I/σ(I): 12.7
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 2.421 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 964 / CC1/2: 0.401 / Rpim(I) all: 1.354 / Rrim(I) all: 2.615 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDS20230630data reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→14.62 Å / SU ML: 0.2075 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3019
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1965 710 5.34 %
Rwork0.1761 12598 -
obs0.1772 13308 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.13 Å2
Refinement stepCycle: LAST / Resolution: 2→14.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 0 21 35 1292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751291
X-RAY DIFFRACTIONf_angle_d0.82321750
X-RAY DIFFRACTIONf_chiral_restr0.0541201
X-RAY DIFFRACTIONf_plane_restr0.0062224
X-RAY DIFFRACTIONf_dihedral_angle_d15.6642491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.150.30761440.2692473X-RAY DIFFRACTION99.66
2.15-2.370.23691400.23652454X-RAY DIFFRACTION100
2.37-2.710.23921640.2512486X-RAY DIFFRACTION99.96
2.71-3.410.25231280.19532540X-RAY DIFFRACTION100
3.41-14.620.14761340.13692645X-RAY DIFFRACTION99.61
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.322328086554.1285799972-0.3676033981145.45039913843-1.793225991321.2106416897-0.1690247988960.4145134335650.00275053815567-0.3710314920630.0945738128773-0.3570585117440.132729213372-0.1345256079980.08656005781170.731536158973-0.2851316070930.2040683194240.394263073307-0.1148977350980.4333285993623.7290005943-4.95838023762-3.03296406037
24.85275580306-3.295490768210.1986718273989.189356001943.640233814098.40681073641-0.564343767259-0.0323349900655-0.186484297815-0.213641766640.2648167244620.801147888232-0.24296215617-0.8991075191650.3685423320950.366771027608-0.05422644954990.003926042732560.3500638166750.03045117729390.3517801279959.52267703486-1.3367675156911.4480136295
31.517434570360.2295233903181.259465809388.215798929820.3381917132025.07811706955-0.7355472340341.01345089764-0.0461801056642-0.730934493430.486420188521.085075592190.942810651406-1.873195722470.3647066958320.62255548404-0.299737187646-0.03077893453250.733609963355-0.08553487737870.6083746936517.59703293833-8.72776213889-0.843792196421
43.204395665852.67862818065-3.194235555768.4867431607-4.073403343573.78737247366-0.5619186327051.147029457630.41803094746-1.061829156370.7435028743710.7154469052920.89972550109-1.51502011643-0.08372442094950.614099664613-0.303471496082-0.1830718007540.9103161683950.06497173713320.5380325294697.16398800462-5.79522453876-4.41193368909
52.65676495172.21175472767-1.569245083986.49474382916-0.9256705114524.2646570508-0.5168191326890.4534530648340.489843506481-0.5525573210550.4554847404590.567778351533-0.126031664353-1.388907569720.09175536577710.536193884922-0.22457350662-0.03721725008270.571733851365-0.03090313995820.38485304265417.49433905122.50789244547-5.01535762137
64.64220901970.600171898208-1.612807490418.705113467750.462270480026.10030070673-0.3908457184340.304583241466-0.216365783231-0.2431707598850.201276924252-0.5565298980910.241608971595-0.1619713911870.1558452179420.451031428782-0.17282866650.0003397134642590.299645056392-0.04517294600230.32487000056819.7886082199-5.434999038024.84221599723
75.233488159062.16426184281-2.404760202092.58060115946-0.2611596921767.210701041570.0723457027274-0.4249552286820.3301556743741.20216719162-0.378113689644-2.298218420520.3425513154061.38520532290.002817314931290.579631740762-0.0967010841356-0.1374383256890.447126211423-0.02618033244950.62572366845826.7235334728-3.0877312234612.0951867243
85.288162563561.6535189696-0.8357068208315.40434361878-0.2071845226686.19609618669-0.158653545037-0.04856637618670.2730070039141.170940664230.109493691433-0.453541954238-0.406378802029-0.6342842161230.2045771423270.566115627468-0.02959036562160.0186658420580.361077853931-0.07218797380910.34078315086716.3287659397-0.48900732956815.0250796839
99.43087254731-2.826688581311.32705818437.13200253106-0.7621790168084.398715898480.036584307586-0.422281388237-0.8194055036190.534313532267-0.07980181138641.111104518061.28438889142-1.390666332140.06579618500110.863262137528-0.3294214102780.1680576508010.538719569955-0.07519136683140.6543725115948.77544166943-15.556528435212.7873795726
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 19 )2 - 191 - 18
22chain 'A' and (resid 20 through 41 )20 - 4119 - 40
33chain 'A' and (resid 42 through 65 )42 - 6541 - 64
44chain 'A' and (resid 66 through 75 )66 - 7565 - 74
55chain 'A' and (resid 76 through 97 )76 - 9775 - 96
66chain 'A' and (resid 98 through 129 )98 - 12997 - 124
77chain 'A' and (resid 130 through 142 )130 - 142125 - 137
88chain 'A' and (resid 143 through 152 )143 - 152138 - 147
99chain 'A' and (resid 153 through 162 )153 - 162148 - 157

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