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- PDB-6b4s: Crystal Structure of Brazil nut (Bertholletia excelsa) allergen B... -

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Basic information

Entry
Database: PDB / ID: 6b4s
TitleCrystal Structure of Brazil nut (Bertholletia excelsa) allergen Ber e 2
Components11S globulin
KeywordsALLERGEN / seed storage protein / Brazil nut / 11S globulin
Function / homology
Function and homology information


seed development / nutrient reservoir activity
Similarity search - Function
11-S seed storage protein, conserved site / 11-S plant seed storage proteins signature. / 11-S seed storage protein, plant / : / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold ...11-S seed storage protein, conserved site / 11-S plant seed storage proteins signature. / 11-S seed storage protein, plant / : / 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
Biological speciesBertholletia excelsa (Brazil nut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.035 Å
AuthorsZhang, Y.Z. / Guo, F.
CitationJournal: to be published
Title: Crystal Structure of Brazil nut (Bertholletia excelsa) allergen Ber e 2
Authors: Zhang, Y.Z. / Guo, F.
History
DepositionSep 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 11S globulin
B: 11S globulin


Theoretical massNumber of molelcules
Total (without water)95,9682
Polymers95,9682
Non-polymers00
Water1,36976
1
A: 11S globulin
B: 11S globulin

A: 11S globulin
B: 11S globulin

A: 11S globulin
B: 11S globulin


Theoretical massNumber of molelcules
Total (without water)287,9046
Polymers287,9046
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area38000 Å2
ΔGint-160 kcal/mol
Surface area66070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.428, 92.428, 213.189
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein 11S globulin


Mass: 47983.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: seeds / Source: (natural) Bertholletia excelsa (Brazil nut) / Tissue: seed / References: UniProt: Q84ND2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
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: 1.83 Å3/Da / Density % sol: 32.64 % / Mosaicity: 1.511 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.45 M sodium chloride

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-BM11
SYNCHROTRONAPS 22-BM21
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDOct 25, 1996
MARMOSAIC 225 mm CCD2CCDOct 25, 1996
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2Bending magnet
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
Reflection twinOperator: h,-h-k,-l / Fraction: 0.26
ReflectionResolution: 2.03→50 Å / Num. obs: 43199 / % possible obs: 99.2 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.077 / Rrim(I) all: 0.168 / Χ2: 1 / Net I/σ(I): 16.6 / Num. measured all: 204337
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.03-2.074.60.92622310.5360.4911.050.97100
2.07-2.14.60.75721800.5940.4010.8581.003100
2.1-2.144.60.75421480.6610.3970.8531.004100
2.14-2.194.70.84721860.7160.4440.9581.003100
2.19-2.234.70.95921380.7320.5041.0851.008100
2.23-2.294.70.45522070.6130.2370.5141.001100
2.29-2.344.70.69921890.7860.3620.7881.005100
2.34-2.414.80.3721620.8680.1910.4171.005100
2.41-2.484.80.32521510.8990.1670.3660.998100
2.48-2.564.80.28122090.8990.1450.3171.013100
2.56-2.654.80.25121400.9050.1290.2831.007100
2.65-2.764.80.21321900.9370.110.240.995100
2.76-2.884.80.19421850.9380.10.2180.98100
2.88-3.034.80.18321790.9450.0930.2060.977100
3.03-3.224.80.16221610.9530.0830.1820.977100
3.22-3.474.80.15121700.9590.0770.171.006100
3.47-3.824.80.14521740.960.0740.1631.031100
3.82-4.374.70.13621710.9590.070.1531.00798.9
4.37-5.514.70.12521170.9660.0650.1410.9997.3
5.51-504.40.10919110.9690.0580.1241.01587.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.035→46.214 Å / Cross valid method: FREE R-VALUE / σ(F): 36.94 / Phase error: 43.08
RfactorNum. reflection% reflection
Rfree0.2696 2020 4.68 %
Rwork0.2502 --
obs0.2601 43163 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 194.37 Å2 / Biso mean: 57.93 Å2 / Biso min: 29.74 Å2
Refinement stepCycle: final / Resolution: 2.035→46.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5542 0 0 76 5618
Biso mean---52.54 -
Num. residues----715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045645
X-RAY DIFFRACTIONf_angle_d0.7017666
X-RAY DIFFRACTIONf_chiral_restr0.093868
X-RAY DIFFRACTIONf_plane_restr0.0031014
X-RAY DIFFRACTIONf_dihedral_angle_d17.0653384
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0366-2.08760.32871580.3418295795
2.0876-2.1440.37291240.3508298996
2.144-2.20710.46521690.4214294594
2.2071-2.27830.43741360.4334297695
2.2783-2.35970.45511290.5072294295
2.3597-2.45410.38851360.3607294796
2.4541-2.56570.38721440.3774298795
2.5657-2.70090.36151470.3468295995
2.7009-2.870.3521460.3213295695
2.87-3.09130.27821300.2881296396
3.0913-3.4020.23761490.2478294995
3.402-3.89330.22511470.2036295795
3.8933-4.90130.20341600.1635288493
4.9013-29.10750.29211380.2174268486
Refinement TLS params.Method: refined / Origin x: -12.3948 Å / Origin y: 35.5099 Å / Origin z: 39.4326 Å
111213212223313233
T0.2949 Å2-0.0444 Å20.0118 Å2-0.3172 Å20.039 Å2--0.3783 Å2
L0.6801 °2-0.0552 °2-0.0384 °2-0.7429 °20.0375 °2--0.5247 °2
S-0.008 Å °-0.0316 Å °-0.1566 Å °0.0158 Å °-0.0209 Å °0.0443 Å °0.1625 Å °-0.1036 Å °0.0437 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA29 - 454
2X-RAY DIFFRACTION1allB30 - 454
3X-RAY DIFFRACTION1allS1 - 76

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