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- PDB-8a0d: Crystal structure of the major guinea pig allergen Cav p 1.0101 p... -

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Basic information

Entry
Database: PDB / ID: 8a0d
TitleCrystal structure of the major guinea pig allergen Cav p 1.0101 part of the lipocalin family
ComponentsAllergen lipocalin Cav p 1 isoform 1
KeywordsALLERGEN / mammalian respiratory allergens
Function / homologyLipocalin, OBP-like / odorant binding / Lipocalin / small molecule binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / extracellular space / Allergen lipocalin Cav p 1 isoform 1
Function and homology information
Biological speciesCavia porcellus (domestic guinea pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.685 Å
AuthorsHerman, R. / Charlier, P. / Janssen-Weets, B. / Hilger, C. / Swiontek, K.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS) Belgium
CitationJournal: Front Allergy / Year: 2022
Title: Mammalian derived lipocalin and secretoglobin respiratory allergens strongly bind ligands with potentially immune modulating properties.
Authors: Janssen-Weets, B. / Kerff, F. / Swiontek, K. / Kler, S. / Czolk, R. / Revets, D. / Kuehn, A. / Bindslev-Jensen, C. / Ollert, M. / Hilger, C.
History
DepositionMay 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / Item: _citation.journal_id_ISSN
Revision 1.2Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Allergen lipocalin Cav p 1 isoform 1
B: Allergen lipocalin Cav p 1 isoform 1
C: Allergen lipocalin Cav p 1 isoform 1
D: Allergen lipocalin Cav p 1 isoform 1
E: Allergen lipocalin Cav p 1 isoform 1


Theoretical massNumber of molelcules
Total (without water)89,0335
Polymers89,0335
Non-polymers00
Water00
1
A: Allergen lipocalin Cav p 1 isoform 1


Theoretical massNumber of molelcules
Total (without water)17,8071
Polymers17,8071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Allergen lipocalin Cav p 1 isoform 1


Theoretical massNumber of molelcules
Total (without water)17,8071
Polymers17,8071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Allergen lipocalin Cav p 1 isoform 1


Theoretical massNumber of molelcules
Total (without water)17,8071
Polymers17,8071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Allergen lipocalin Cav p 1 isoform 1


Theoretical massNumber of molelcules
Total (without water)17,8071
Polymers17,8071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Allergen lipocalin Cav p 1 isoform 1


Theoretical massNumber of molelcules
Total (without water)17,8071
Polymers17,8071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.44, 122.85, 123.36
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Allergen lipocalin Cav p 1 isoform 1


Mass: 17806.502 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Gene: lcn / Production host: Escherichia coli (E. coli) / Variant (production host): pET-21d(+) / References: UniProt: A0A484HM70
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: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 250 nl protein 4 mg/mL Tris-HCl 20 mM pH 7, 250 nl polyvinylpyrrolidone K15 50% w/v, citrate 0.1M pH 5, 50 nL of 6-Aminohexanoic acid 30% w/v and 50 nL of 1-decanol 1 mM in ethanol 1% v/v

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.685→47.5 Å / Num. obs: 12775 / % possible obs: 99.9 % / Redundancy: 13.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.272 / Net I/σ(I): 10.2
Reflection shellResolution: 3.7→3.78 Å / Redundancy: 12 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 922 / CC1/2: 0.87 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E5P

1e5p


Resolution: 3.685→29.91 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.871 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.642
RfactorNum. reflection% reflectionSelection details
Rfree0.2619 635 -RANDOM
Rwork0.2563 ---
obs0.2566 12708 100 %-
Displacement parametersBiso mean: 94.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.0088 Å20 Å20 Å2
2--0.6231 Å20 Å2
3----0.6319 Å2
Refine analyzeLuzzati coordinate error obs: 0.55 Å
Refinement stepCycle: LAST / Resolution: 3.685→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5815 0 0 0 5815
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00711405HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9220555HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3465SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1870HARMONIC5
X-RAY DIFFRACTIONt_it5925HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion790SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8404SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion17.37
LS refinement shellResolution: 3.69→3.73 Å
RfactorNum. reflection% reflection
Rfree0.2563 20 -
Rwork0.3422 --
obs0.338 410 99.76 %

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