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- PDB-7u1h: Crystal structure of Lens culinaris vicilin -

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Basic information

Entry
Database: PDB / ID: 7u1h
TitleCrystal structure of Lens culinaris vicilin
ComponentsAllergen Len c 1.0101
KeywordsALLERGEN / Cupin / Vicilin / Convicilin / Lentil / Seed Storage Protein
Function / homologyCupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / Allergen Len c 1.0101
Function and homology information
Biological speciesLens culinaris (lentil)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRobinson, K.A. / Bakestani, I.D. / Loewen, M.C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Other government Canada
CitationJournal: Food Chem (Oxf) / Year: 2022
Title: Pea and lentil 7S globulin crystal structures with comparative immunoglobulin epitope mapping.
Authors: Robinson, K.A. / St-Jacques, A.D. / Bakestani, I.D. / Beavington, B.A.G. / Loewen, M.C.
History
DepositionFeb 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Allergen Len c 1.0101
B: Allergen Len c 1.0101
C: Allergen Len c 1.0101


Theoretical massNumber of molelcules
Total (without water)148,1343
Polymers148,1343
Non-polymers00
Water72140
1
B: Allergen Len c 1.0101
C: Allergen Len c 1.0101

A: Allergen Len c 1.0101


Theoretical massNumber of molelcules
Total (without water)148,1343
Polymers148,1343
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area14810 Å2
ΔGint-79 kcal/mol
Surface area40260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.441, 92.504, 143.738
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Allergen Len c 1.0101


Mass: 49377.871 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lens culinaris (lentil)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q84UI1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.01 M Zinc Chloride, 0.1 M Sodium acetate trihydrate, 15% PEG6000, with 20% glycerol as cryoprotectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→143.74 Å / Num. obs: 39945 / % possible obs: 98.6 % / Redundancy: 6.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.093 / Rrim(I) all: 0.172 / Net I/σ(I): 9.6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.782 / Num. unique obs: 4426 / CC1/2: 0.812 / Rpim(I) all: 0.513 / Rrim(I) all: 0.939

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UIK

1uik


Resolution: 2.5→77.909 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.878 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.181 / SU B: 12.975 / SU ML: 0.281 / Average fsc free: 0.8585 / Average fsc work: 0.8906 / Cross valid method: NONE / ESU R: 0.939 / ESU R Free: 0.351
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2839 2073 5.197 %
Rwork0.1992 37814 -
all0.204 --
obs-39887 98.239 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.052 Å2
Baniso -1Baniso -2Baniso -3
1-5.473 Å2-0 Å20 Å2
2---2.584 Å20 Å2
3----2.889 Å2
Refinement stepCycle: LAST / Resolution: 2.5→77.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8688 0 0 40 8728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138924
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158621
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.6412074
X-RAY DIFFRACTIONr_angle_other_deg1.2041.58219808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.32151106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87222.991535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.473151590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.331567
X-RAY DIFFRACTIONr_chiral_restr0.0680.21164
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210311
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022167
X-RAY DIFFRACTIONr_nbd_refined0.2150.21707
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.28353
X-RAY DIFFRACTIONr_nbtor_refined0.1640.24057
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.24894
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2214
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1310.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2290.260
X-RAY DIFFRACTIONr_nbd_other0.2260.2266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.230.215
X-RAY DIFFRACTIONr_mcbond_it2.8743.5974388
X-RAY DIFFRACTIONr_mcbond_other2.8743.5974387
X-RAY DIFFRACTIONr_mcangle_it4.5395.3855476
X-RAY DIFFRACTIONr_mcangle_other4.5395.3855477
X-RAY DIFFRACTIONr_scbond_it3.2493.9774536
X-RAY DIFFRACTIONr_scbond_other3.2483.9774537
X-RAY DIFFRACTIONr_scangle_it5.2725.7996588
X-RAY DIFFRACTIONr_scangle_other5.2725.7996589
X-RAY DIFFRACTIONr_lrange_it7.77741.6019234
X-RAY DIFFRACTIONr_lrange_other7.77741.6039235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.3671510.292733X-RAY DIFFRACTION97.7627
2.565-2.6350.361540.2732682X-RAY DIFFRACTION97.9958
2.635-2.7120.3641500.2522602X-RAY DIFFRACTION97.9708
2.712-2.7950.3691280.2332555X-RAY DIFFRACTION97.9912
2.795-2.8870.2771230.2092465X-RAY DIFFRACTION97.7711
2.887-2.9880.3341420.22354X-RAY DIFFRACTION97.844
2.988-3.1010.271510.1772276X-RAY DIFFRACTION98.021
3.101-3.2270.3041180.2032233X-RAY DIFFRACTION98.4918
3.227-3.3710.314890.2072156X-RAY DIFFRACTION98.3355
3.371-3.5350.293970.192063X-RAY DIFFRACTION98.3159
3.535-3.7260.288910.1981997X-RAY DIFFRACTION98.3051
3.726-3.9520.27860.1871850X-RAY DIFFRACTION98.8764
3.952-4.2250.221820.1581775X-RAY DIFFRACTION98.4102
4.225-4.5630.255990.1551642X-RAY DIFFRACTION99.1458
4.563-4.9980.184910.1511492X-RAY DIFFRACTION98.323
4.998-5.5870.295930.2071363X-RAY DIFFRACTION98.913
5.587-6.4490.304780.2041218X-RAY DIFFRACTION98.9313
6.449-7.8950.301640.2141054X-RAY DIFFRACTION98.7633

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