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- PDB-7u1j: Crystal structure of Pisum sativum convicilin -

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Basic information

Entry
Database: PDB / ID: 7u1j
TitleCrystal structure of Pisum sativum convicilin
ComponentsConvicilin
KeywordsALLERGEN / Cupin / Vicilin / Convicilin / Pea / Seed Storage Protein
Function / homology
Function and homology information


aleurone grain / nutrient reservoir activity / vacuole
Similarity search - Function
: / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsBakestani, I.D. / Robinson, K.A. / 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 30, 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: Convicilin
B: Convicilin
C: Convicilin


Theoretical massNumber of molelcules
Total (without water)142,3213
Polymers142,3213
Non-polymers00
Water2,162120
1
A: Convicilin

A: Convicilin

A: Convicilin


Theoretical massNumber of molelcules
Total (without water)142,3213
Polymers142,3213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
Buried area14670 Å2
ΔGint-81 kcal/mol
Surface area40050 Å2
MethodPISA
2
B: Convicilin

B: Convicilin

B: Convicilin


Theoretical massNumber of molelcules
Total (without water)142,3213
Polymers142,3213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_544z,-x-1/2,-y-1/21
crystal symmetry operation48_445-y-1/2,-z-1/2,x1
Buried area14370 Å2
ΔGint-82 kcal/mol
Surface area39800 Å2
MethodPISA
3
C: Convicilin

C: Convicilin

C: Convicilin


Theoretical massNumber of molelcules
Total (without water)142,3213
Polymers142,3213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area14390 Å2
ΔGint-87 kcal/mol
Surface area40050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)269.155, 269.155, 269.155
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23

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Components

#1: Protein Convicilin


Mass: 47440.441 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: cvc
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9M3X6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.03 Å3/Da / Density % sol: 59.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.15M Ammonium Acetate, 25% PEG3350, 0.05M Bis Tris

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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 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→134.941 Å / Num. obs: 44137 / % possible obs: 99.8 % / Redundancy: 5.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.081 / Rrim(I) all: 0.151 / Net I/σ(I): 8.9
Reflection shellResolution: 2.7→2.81 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.554 / Num. unique obs: 4997 / CC1/2: 0.811 / Rpim(I) all: 0.359 / Rrim(I) all: 0.663

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Processing

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

1uik


Resolution: 2.701→134.941 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.863 / WRfactor Rfree: 0.27 / WRfactor Rwork: 0.204 / SU B: 13.705 / SU ML: 0.28 / Average fsc free: 0.8761 / Average fsc work: 0.8982 / Cross valid method: NONE / ESU R: 0.604 / ESU R Free: 0.347
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.281 2246 5.089 %
Rwork0.2149 41888 -
all0.218 --
obs-44134 99.772 %
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: 43.743 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.701→134.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8329 0 0 120 8449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138475
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158209
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.63911463
X-RAY DIFFRACTIONr_angle_other_deg1.2231.58118875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.56151027
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47723.633490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.004151516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1631551
X-RAY DIFFRACTIONr_chiral_restr0.0750.21087
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021950
X-RAY DIFFRACTIONr_nbd_refined0.2240.21619
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.28021
X-RAY DIFFRACTIONr_nbtor_refined0.1690.23799
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.24940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0680.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1710.279
X-RAY DIFFRACTIONr_nbd_other0.1980.2323
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1830.221
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0450.21
X-RAY DIFFRACTIONr_mcbond_it4.0964.3634144
X-RAY DIFFRACTIONr_mcbond_other4.0964.3634143
X-RAY DIFFRACTIONr_mcangle_it6.286.5235159
X-RAY DIFFRACTIONr_mcangle_other6.286.5245160
X-RAY DIFFRACTIONr_scbond_it4.444.8874331
X-RAY DIFFRACTIONr_scbond_other4.444.8874332
X-RAY DIFFRACTIONr_scangle_it6.967.1246304
X-RAY DIFFRACTIONr_scangle_other6.9597.1246305
X-RAY DIFFRACTIONr_lrange_it9.66749.7368719
X-RAY DIFFRACTIONr_lrange_other9.66649.748719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.701-2.7710.3841510.3043097X-RAY DIFFRACTION100
2.771-2.8470.3621660.2612982X-RAY DIFFRACTION100
2.847-2.9290.3341360.2472978X-RAY DIFFRACTION99.9679
2.929-3.0190.2991330.2312864X-RAY DIFFRACTION100
3.019-3.1180.3091400.2432762X-RAY DIFFRACTION100
3.118-3.2280.3311400.2432675X-RAY DIFFRACTION100
3.228-3.3490.2871430.2292549X-RAY DIFFRACTION100
3.349-3.4860.2721270.2172483X-RAY DIFFRACTION100
3.486-3.6410.2851250.2182367X-RAY DIFFRACTION100
3.641-3.8190.3151200.2172283X-RAY DIFFRACTION100
3.819-4.0250.2551440.1952095X-RAY DIFFRACTION97.0525
4.025-4.2690.2661120.1862040X-RAY DIFFRACTION99.9536
4.269-4.5640.241220.1771902X-RAY DIFFRACTION100
4.564-4.9290.2661010.171804X-RAY DIFFRACTION100
4.929-5.3990.2281150.1831625X-RAY DIFFRACTION100
5.399-6.0350.249800.2061502X-RAY DIFFRACTION100
6.035-6.9670.28820.2091332X-RAY DIFFRACTION100
6.967-8.5280.302560.1921137X-RAY DIFFRACTION99.6658

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