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- PDB-9i7n: Beta-lactoglobulin complex with retinol post lyophilization -

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Basic information

Entry
Database: PDB / ID: 9i7n
TitleBeta-lactoglobulin complex with retinol post lyophilization
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: 1.95 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
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.749, 53.749, 113.063
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.: 30 / 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: 47.85 %
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: Oct 25, 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: 1.95→14.65 Å / Num. obs: 14354 / % possible obs: 99.7 % / Redundancy: 8.3 % / Biso Wilson estimate: 35.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.03 / Rrim(I) all: 0.086 / Net I/σ(I): 15.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.338 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 993 / CC1/2: 0.538 / Rpim(I) all: 0.566 / Rrim(I) all: 1.457 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDS20230630data reduction
Aimless0.8.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→14.65 Å / SU ML: 0.1664 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.5238
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.211 689 4.83 %
Rwork0.179 13572 -
obs0.1806 14261 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.37 Å2
Refinement stepCycle: LAST / Resolution: 1.95→14.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 0 21 30 1287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01161291
X-RAY DIFFRACTIONf_angle_d1.27231750
X-RAY DIFFRACTIONf_chiral_restr0.0788201
X-RAY DIFFRACTIONf_plane_restr0.0097224
X-RAY DIFFRACTIONf_dihedral_angle_d16.6478491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.10.28451140.23322671X-RAY DIFFRACTION99.75
2.1-2.310.25881500.21042673X-RAY DIFFRACTION99.89
2.31-2.640.24711340.23112692X-RAY DIFFRACTION99.61
2.64-3.320.21941450.21042716X-RAY DIFFRACTION99.2
3.32-14.650.18521460.14332820X-RAY DIFFRACTION98.9
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)
12.696285698912.148482493360.194196870254.501673912111.182753882510.395907151711-0.2772864117630.3282697071-0.157789974275-0.4387574933840.2268629663470.136957442997-0.110843229945-0.01546682501820.2001112730850.667392925763-0.328278632068-0.2066716834050.3389023934090.124049940210.426883950055-23.56543903335.03544565824-3.06925367872
25.37603005729-3.8689924544-1.222648772438.58924219487-4.051368383544.77763647467-0.620086988875-0.2062779377510.331325567964-0.271716864850.341378110004-0.7895870089480.10533941860.68885685760.2740217521940.409799571323-0.0551229620641-0.01448857609010.275786963318-0.05095328555170.276306256641-9.504940057151.1968140013111.7777483432
30.0862986473862-0.4788132922210.4053501095722.69017622058-2.283803772761.94057834093-0.6036641865820.8824189726270.0333916860181-1.028464077830.242838068598-0.379980822058-0.1035257158390.9727358745360.4040782376710.83910890535-0.321179799588-3.14229337055E-50.5958326045410.08133915292710.404931509029-12.61004595479.4018316327-5.1273586057
45.972877452121.316706635244.046762152329.498030548413.497139170286.47459806286-0.6285960920730.594416312159-0.2241762090780.4350577356030.127764293502-1.48109936494-0.3783438333161.608700027330.6138883022940.502012910734-0.268702295373-0.04150029403090.8362744880250.1500731053410.615365549746-2.551737934477.94775648783.79943560526
51.160537187481.466316085831.231631215194.903091746684.744606814494.64309953058-0.7392013964120.999037328116-0.338765794652-1.096262705360.860454850708-0.614283618833-1.166072567811.587054001050.05473647500470.635755873133-0.3372712739860.08581043310810.820873079857-0.0448690629490.55752243396-6.887279561475.82080437858-4.28394226893
61.64793185720.9812884526171.423163336316.320187611991.324116034324.62545494565-0.5240140536750.56926619121-0.21108106494-0.6566323254190.398826473802-0.351190542330.175766509881.108791098480.04686750130070.511270441626-0.2596388349530.04318648404440.4335339779060.008508186508620.272701909636-17.3075284923-2.51898778895-5.01062319112
73.729981630951.849166739891.571521990035.16705998066-0.7541475365415.08097043547-0.2484832568960.297362421450.141637087271-0.2415803231950.097697327930.352988892596-0.134597183410.06054337270980.1198124423140.421640114394-0.1576067855-0.03178780832540.2307074368470.05877308903780.261206215914-19.67556165455.462890866924.84425419132
85.298942132371.603741112362.409863920591.76289968442-1.200810399395.41940236750.000353841315714-0.458321489785-0.6861070310831.05829915982-0.1065188926931.485956002740.314943448044-1.09855751028-0.00158556096690.460916888059-0.1140619716520.1351592320350.3787025928420.04456824136470.462627990294-26.70788451013.1301319360312.0509862786
92.04095409563-1.04706962258-1.410879100056.255086985870.4021087304443.39178338265-0.132081894611-0.0951422882440.2664623530030.5216914742530.0426718628831-0.489163267235-0.455174704080.7016369725380.02785275482310.568056763544-0.148891720465-0.1478808503390.3514077422470.0840075093550.382877322319-12.53674691288.043925432813.9862078492
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 40 )20 - 4019 - 39
33chain 'A' and (resid 41 through 53 )41 - 5340 - 52
44chain 'A' and (resid 54 through 65 )54 - 6553 - 64
55chain 'A' and (resid 66 through 75 )66 - 7565 - 74
66chain 'A' and (resid 76 through 97 )76 - 9775 - 96
77chain 'A' and (resid 98 through 129 )98 - 12997 - 124
88chain 'A' and (resid 130 through 142 )130 - 142125 - 137
99chain 'A' and (resid 143 through 162 )143 - 162138 - 157

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