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- PDB-7u1i: Crystal structure of Pisum sativum vicilin -

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Basic information

Entry
Database: PDB / ID: 7u1i
TitleCrystal structure of Pisum sativum vicilin
ComponentsVicilin
KeywordsALLERGEN / Pisum Sativum / Pis s 1 / Vicilin / Seed Storage Protein
Function / homologyCupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / Vicilin
Function and homology information
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBeavington, B.A.G. / Bakestani, I.D. / Robinson, K.A. / Loewen, M.C.
Funding support1items
OrganizationGrant numberCountry
Other government
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 16, 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: Vicilin
B: Vicilin
C: Vicilin


Theoretical massNumber of molelcules
Total (without water)146,3593
Polymers146,3593
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14310 Å2
ΔGint-81 kcal/mol
Surface area39690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.316, 52.688, 127.844
Angle α, β, γ (deg.)90.000, 95.193, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Vicilin /


Mass: 48786.293 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q702P1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.075M Sodium fluoride, 0.1M Bis-tris propane, 10% PEG3350

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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: 3.1→98.104 Å / Num. obs: 20422 / % possible obs: 85.9 % / Redundancy: 3 % / CC1/2: 0.985 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.099 / Rrim(I) all: 0.142 / Net I/σ(I): 6
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.288 / Num. unique obs: 20422 / CC1/2: 0.878 / Rpim(I) all: 0.278 / Rrim(I) all: 0.401

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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: 3.1→98.104 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.835 / WRfactor Rfree: 0.271 / WRfactor Rwork: 0.177 / SU B: 26.175 / SU ML: 0.449 / Average fsc free: 0.8659 / Average fsc work: 0.9043 / Cross valid method: NONE / ESU R Free: 0.63
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.285 1022 5.007 %
Rwork0.1847 19391 -
all0.19 --
obs-20413 84.386 %
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: 46.421 Å2
Baniso -1Baniso -2Baniso -3
1--2.951 Å20 Å2-2.324 Å2
2--1.555 Å20 Å2
3---1.788 Å2
Refinement stepCycle: LAST / Resolution: 3.1→98.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8488 0 0 20 8508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0138633
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168297
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.63411682
X-RAY DIFFRACTIONr_angle_other_deg1.1131.57919067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1751070
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45724.083480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.108151490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8761544
X-RAY DIFFRACTIONr_chiral_restr0.0510.21123
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029976
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022024
X-RAY DIFFRACTIONr_nbd_refined0.2160.21913
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.28719
X-RAY DIFFRACTIONr_nbtor_refined0.1650.24013
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.24599
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2218
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0730.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2190.23
X-RAY DIFFRACTIONr_nbd_other0.2670.210
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.21
X-RAY DIFFRACTIONr_mcbond_it3.0494.8444313
X-RAY DIFFRACTIONr_mcbond_other3.0494.8444312
X-RAY DIFFRACTIONr_mcangle_it4.9827.2565372
X-RAY DIFFRACTIONr_mcangle_other4.9817.2575373
X-RAY DIFFRACTIONr_scbond_it2.8625.0664320
X-RAY DIFFRACTIONr_scbond_other2.8625.0664321
X-RAY DIFFRACTIONr_scangle_it4.8097.4916310
X-RAY DIFFRACTIONr_scangle_other4.8097.4916311
X-RAY DIFFRACTIONr_lrange_it7.73456.8249209
X-RAY DIFFRACTIONr_lrange_other7.73456.8229209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.371810.2871382X-RAY DIFFRACTION84.6644
3.18-3.2670.304640.2431483X-RAY DIFFRACTION87.9977
3.267-3.3620.364770.221357X-RAY DIFFRACTION86.8039
3.362-3.4660.347690.2281325X-RAY DIFFRACTION85.7319
3.466-3.5790.308580.2251318X-RAY DIFFRACTION86.6499
3.579-3.7050.32830.2081247X-RAY DIFFRACTION87.156
3.705-3.8440.292530.1861226X-RAY DIFFRACTION86.1279
3.844-4.0010.269700.1691161X-RAY DIFFRACTION85.6646
4.001-4.1790.25520.1581074X-RAY DIFFRACTION84.4711
4.179-4.3830.225480.1521048X-RAY DIFFRACTION82.5301
4.383-4.6190.26620.142980X-RAY DIFFRACTION83.4936
4.619-4.8990.243490.146961X-RAY DIFFRACTION84.6605
4.899-5.2370.31480.155874X-RAY DIFFRACTION82.8392
5.237-5.6560.209390.164827X-RAY DIFFRACTION83.1094
5.656-6.1940.251350.174767X-RAY DIFFRACTION83.2814
6.194-6.9230.4380.185667X-RAY DIFFRACTION80.5714
6.923-7.990.256340.17576X-RAY DIFFRACTION78.4062
7.99-9.7770.215310.149506X-RAY DIFFRACTION80.6306

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