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- PDB-8ofd: Crystal structure of beta-conglutin from Lupinus albus refined to... -

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Basic information

Entry
Database: PDB / ID: 8ofd
TitleCrystal structure of beta-conglutin from Lupinus albus refined to 2.81 A
ComponentsConglutin beta 1
KeywordsALLERGEN / beta-conglutin / Lup an 1 / seed storage protein
Function / homology
Function and homology information


nutrient reservoir activity
Similarity search - Function
: / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / : / Conglutin beta 1
Similarity search - Component
Biological speciesLupinus albus (white lupine)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsDolot, R.M. / O'Sullivan, C.K. / Jauset-Rubio, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: First crystal structure of beta-conglutin, a major lupin allergen from Lupinus albus seeds
Authors: Dolot, R.M. / O'Sullivan, C.K. / Jauset-Rubio, M.
History
DepositionMar 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conglutin beta 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1514
Polymers49,0301
Non-polymers1213
Water1,47782
1
A: Conglutin beta 1
hetero molecules

A: Conglutin beta 1
hetero molecules

A: Conglutin beta 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,45312
Polymers147,0903
Non-polymers3639
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Unit cell
Length a, b, c (Å)166.630, 166.630, 40.098
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-602-

NA

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Components

#1: Protein Conglutin beta 1 / Protein Lup-1


Mass: 49029.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 1-30 - signal protein (not present) 31-108 - propeptide (not present) 109-531 - conglutin beta 1. Residues 408-415 and 518-531 not included. Residue 176 changed from L to I based on experimental data.
Source: (natural) Lupinus albus (white lupine) / References: UniProt: Q53HY0
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.38 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 40% (v/v) Tacsimate pH 7.0, 50 mM HEPES pH 7.0, 2 mM Spermine, and 2 mM Hexaamine cobalt (III)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.81→21.77 Å / Num. obs: 15700 / % possible obs: 99.7 % / Redundancy: 7.8 % / Biso Wilson estimate: 55 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.064 / Rrim(I) all: 0.182 / Χ2: 0.93 / Net I/σ(I): 9.1
Reflection shellResolution: 2.81→2.96 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.001 / Mean I/σ(I) obs: 2 / Num. unique obs: 2263 / CC1/2: 0.657 / Rpim(I) all: 0.366 / Rrim(I) all: 1.067 / Χ2: 0.92 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
CrysalisPro1.171.41.100data reduction
Aimless0.7.9data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→21.767 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.844 / WRfactor Rfree: 0.258 / WRfactor Rwork: 0.192 / SU B: 14.27 / SU ML: 0.303 / Average fsc free: 0.9384 / Average fsc work: 0.9696 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.08
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2772 774 4.934 %
Rwork0.204 14912 -
all0.208 --
obs-15686 99.771 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 62.202 Å2
Baniso -1Baniso -2Baniso -3
1-0.895 Å20 Å20 Å2
2--0.895 Å20 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 2.81→21.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 6 82 3369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123367
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163139
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.6574553
X-RAY DIFFRACTIONr_angle_other_deg0.4391.577195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7485403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.377533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.80410586
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.93210199
X-RAY DIFFRACTIONr_chiral_restr0.0580.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02874
X-RAY DIFFRACTIONr_nbd_refined0.2280.2803
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2180.23373
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21613
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22074
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2141
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0510.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2210.250
X-RAY DIFFRACTIONr_nbd_other0.2420.2162
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.250.29
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1590.21
X-RAY DIFFRACTIONr_mcbond_it4.9556.2111613
X-RAY DIFFRACTIONr_mcbond_other4.9416.2121612
X-RAY DIFFRACTIONr_mcangle_it7.67311.1422015
X-RAY DIFFRACTIONr_mcangle_other7.67211.1442016
X-RAY DIFFRACTIONr_scbond_it5.086.6591754
X-RAY DIFFRACTIONr_scbond_other5.0796.6581755
X-RAY DIFFRACTIONr_scangle_it7.90412.0032538
X-RAY DIFFRACTIONr_scangle_other7.90312.0022539
X-RAY DIFFRACTIONr_lrange_it12.23873.0263888
X-RAY DIFFRACTIONr_lrange_other12.24373.0873883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.8820.442570.2431077X-RAY DIFFRACTION99.561
2.882-2.9590.333780.2311009X-RAY DIFFRACTION100
2.959-3.0430.412450.2181037X-RAY DIFFRACTION99.9077
3.043-3.1350.265400.2271017X-RAY DIFFRACTION99.9055
3.135-3.2360.327510.212945X-RAY DIFFRACTION100
3.236-3.3470.29510.187963X-RAY DIFFRACTION99.9015
3.347-3.470.271420.197879X-RAY DIFFRACTION100
3.47-3.6080.256440.208899X-RAY DIFFRACTION100
3.608-3.7630.236380.196820X-RAY DIFFRACTION100
3.763-3.9410.314440.199817X-RAY DIFFRACTION99.884
3.941-4.1470.262500.195745X-RAY DIFFRACTION100
4.147-4.3880.266350.176742X-RAY DIFFRACTION100
4.388-4.6780.218460.161669X-RAY DIFFRACTION100
4.678-5.0330.233240.181679X-RAY DIFFRACTION100
5.033-5.4850.206370.199562X-RAY DIFFRACTION100
5.485-6.0840.229150.229570X-RAY DIFFRACTION100
6.084-6.9350.321320.228483X-RAY DIFFRACTION100
6.935-8.2860.319140.223437X-RAY DIFFRACTION99.3392
8.286-10.9520.249130.221342X-RAY DIFFRACTION99.162
10.952-21.7670.346180.311220X-RAY DIFFRACTION91.8919

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