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- PDB-3smh: Crystal structure of major peanut allergen Ara h 1 -

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Basic information

Entry
Database: PDB / ID: 3smh
TitleCrystal structure of major peanut allergen Ara h 1
ComponentsAllergen Ara h 1, clone P41B
KeywordsALLERGEN / Cupin fold
Function / homology
Function and homology information


: / 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
Allergen Ara h 1, clone P41B
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.433 Å
AuthorsCabanos, C.S. / Mikami, B. / Maruyama, N.
Citation
Journal: Mol.Immunol. / Year: 2011
Title: Crystal structure of the major peanut allergen Ara h 1.
Authors: Cabanos, C. / Urabe, H. / Tandang-Silvas, M.R. / Utsumi, S. / Mikami, B. / Maruyama, N.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Crystallization and preliminary X-ray analysis of the major peanut allergen Ara h 1 core region.
Authors: Cabanos, C.S. / Urabe, H. / Masuda, T. / Tandang-Silvas, M.R. / Utsumi, S. / Mikami, B. / Maruyama, N.
History
DepositionJun 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Non-polymer description
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Allergen Ara h 1, clone P41B
B: Allergen Ara h 1, clone P41B
C: Allergen Ara h 1, clone P41B
D: Allergen Ara h 1, clone P41B
E: Allergen Ara h 1, clone P41B
F: Allergen Ara h 1, clone P41B


Theoretical massNumber of molelcules
Total (without water)285,3896
Polymers285,3896
Non-polymers00
Water6,071337
1
A: Allergen Ara h 1, clone P41B
C: Allergen Ara h 1, clone P41B
D: Allergen Ara h 1, clone P41B


Theoretical massNumber of molelcules
Total (without water)142,6953
Polymers142,6953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15510 Å2
ΔGint-84 kcal/mol
Surface area39070 Å2
MethodPISA
2
B: Allergen Ara h 1, clone P41B
E: Allergen Ara h 1, clone P41B
F: Allergen Ara h 1, clone P41B


Theoretical massNumber of molelcules
Total (without water)142,6953
Polymers142,6953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14750 Å2
ΔGint-89 kcal/mol
Surface area38360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.492, 89.008, 158.966
Angle α, β, γ (deg.)90.00, 107.15, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 3:171 OR RESSEQ 194:209 OR RESSEQ 219:298 OR RESSEQ 327:416 )
211CHAIN B AND (RESSEQ 3:171 OR RESSEQ 194:209 OR RESSEQ 222:298 OR RESSEQ 327:416 )
311CHAIN C AND (RESSEQ 3:171 OR RESSEQ 194:209 OR RESSEQ 221:298 OR RESSEQ 327:416 )
411CHAIN D AND (RESSEQ 3:171 OR RESSEQ 194:209 OR RESSEQ 223:298 OR RESSEQ 327:416 )
511CHAIN E AND (RESSEQ 3:171 OR RESSEQ 194:209 OR RESSEQ 219:298 OR RESSEQ 327:416 )
611CHAIN F AND (RESSEQ 3:171 OR RESSEQ 194:209 OR RESSEQ 221:298 OR RESSEQ 327:416 )

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Components

#1: Protein
Allergen Ara h 1, clone P41B / Allergen Ara h I


Mass: 47564.863 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 170-587
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arachis hypogaea (peanut) / Gene: Arachis hypogea / Production host: Escherichia coli (E. coli) / References: UniProt: P43238
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 1.85 Å3/Da / Density % sol: 33.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate pH 5.6, 0.1M NaCl, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.43→15 Å / Num. obs: 122061 / % possible obs: 99 % / Observed criterion σ(F): 14 / Observed criterion σ(I): 5.45
Reflection shellResolution: 2.43→2.46 Å / % possible all: 93

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
PHENIX(phenix.refine: 1.6.4_486)refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.433→14.996 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 3859 5.03 %RANDOM
Rwork0.2015 ---
all0.267 ---
obs0.2036 76734 98.28 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.859 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-21.6744 Å20 Å24.0934 Å2
2---7.1356 Å2-0 Å2
3----14.5388 Å2
Refinement stepCycle: LAST / Resolution: 2.433→14.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17613 0 0 337 17950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817907
X-RAY DIFFRACTIONf_angle_d1.07224126
X-RAY DIFFRACTIONf_dihedral_angle_d22.95211220
X-RAY DIFFRACTIONf_chiral_restr0.0722635
X-RAY DIFFRACTIONf_plane_restr0.0043254
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2806X-RAY DIFFRACTIONPOSITIONAL
12B2806X-RAY DIFFRACTIONPOSITIONAL0.058
13C2815X-RAY DIFFRACTIONPOSITIONAL0.048
14D2797X-RAY DIFFRACTIONPOSITIONAL0.055
15E2830X-RAY DIFFRACTIONPOSITIONAL0.053
16F2815X-RAY DIFFRACTIONPOSITIONAL0.05
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4334-2.4630.34131300.2662242493
2.463-2.4940.36391260.2668258698
2.494-2.52670.36651560.262256498
2.5267-2.56110.31651270.2528261398
2.5611-2.59750.30161250.2388253798
2.5975-2.63610.31311340.2341258998
2.6361-2.67710.31021300.2472255398
2.6771-2.72070.32911160.2522264497
2.7207-2.76730.31281420.2361257598
2.7673-2.81730.30471450.2242255298
2.8173-2.87110.2761380.2219258498
2.8711-2.92930.29711490.2205255298
2.9293-2.99250.27821410.2173256497
2.9925-3.06160.27551430.2254257098
3.0616-3.13750.28211180.2243261698
3.1375-3.22150.28791430.2271258998
3.2215-3.31530.26181350.215258398
3.3153-3.42110.26471430.2184258698
3.4211-3.54180.23231410.2107262799
3.5418-3.68160.28911660.2052608100
3.6816-3.84650.21821450.19882631100
3.8465-4.04550.1911220.18732673100
4.0455-4.29330.22051380.17022664100
4.2933-4.61590.19121590.16492619100
4.6159-5.06410.17951210.16662693100
5.0641-5.76020.20341390.17892673100
5.7602-7.12520.21941510.19112670100
7.1252-14.99610.17921360.1702273699

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