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- PDB-3s7i: Crystal structure of Ara h 1 -

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Basic information

Entry
Database: PDB / ID: 3s7i
TitleCrystal structure of Ara h 1
ComponentsAllergen Ara h 1, clone P41B
KeywordsALLERGEN / bicupin / vicilin / storage seed protein
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: 2.35 Å
AuthorsChruszcz, M. / Maleki, S.J. / Solberg, R. / Minor, W.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Immunologic Characterization of Ara h 1, a Major Peanut Allergen.
Authors: Chruszcz, M. / Maleki, S.J. / Majorek, K.A. / Demas, M. / Bublin, M. / Solberg, R. / Hurlburt, B.K. / Ruan, S. / Mattisohn, C.P. / Breiteneder, H. / Minor, W.
History
DepositionMay 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Allergen Ara h 1, clone P41B
B: Allergen Ara h 1, clone P41B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2694
Polymers95,1982
Non-polymers712
Water2,396133
1
A: Allergen Ara h 1, clone P41B
hetero molecules

A: Allergen Ara h 1, clone P41B
hetero molecules

A: Allergen Ara h 1, clone P41B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,9036
Polymers142,7973
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area15700 Å2
ΔGint-132 kcal/mol
Surface area39020 Å2
MethodPISA
2
B: Allergen Ara h 1, clone P41B
hetero molecules

B: Allergen Ara h 1, clone P41B
hetero molecules

B: Allergen Ara h 1, clone P41B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,9036
Polymers142,7973
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area14070 Å2
ΔGint-135 kcal/mol
Surface area37800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.886, 92.886, 231.552
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A172 - 586
2111B172 - 586

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Components

#1: Protein Allergen Ara h 1, clone P41B


Mass: 47599.012 Da / Num. of mol.: 2 / Fragment: UNP residues 170-586
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arachis hypogaea (peanut) / Plasmid: pET9a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P43238
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG400, 150 mM NaCl, 100 mM Na citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2011 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.948
11K, H, -L20.052
ReflectionResolution: 2.35→50 Å / Num. all: 31048 / Num. obs: 31048 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 49.3 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 30.6
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1563 / Rsym value: 0.628 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMAC5.5.0109refinement
Cootmodel building
CCP4refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S7E

3s7e


Resolution: 2.35→40.13 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.907 / SU B: 14.601 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24373 1386 5.2 %RANDOM
Rwork0.20273 ---
all0.20489 25512 --
obs0.20489 25512 86.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.129 Å2
Baniso -1Baniso -2Baniso -3
1-8.09 Å20 Å20 Å2
2--8.09 Å20 Å2
3----16.18 Å2
Refinement stepCycle: LAST / Resolution: 2.35→40.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5587 0 2 133 5722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225732
X-RAY DIFFRACTIONr_bond_other_d0.0030.023786
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9427766
X-RAY DIFFRACTIONr_angle_other_deg1.14439243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0595730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.54725.086291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.63115925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0281535
X-RAY DIFFRACTIONr_chiral_restr0.0990.2873
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216548
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021127
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6041.53667
X-RAY DIFFRACTIONr_mcbond_other0.2171.51483
X-RAY DIFFRACTIONr_mcangle_it1.08425859
X-RAY DIFFRACTIONr_scbond_it2.19632065
X-RAY DIFFRACTIONr_scangle_it3.2094.51907
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4426 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.060.05
tight thermal0.170.5
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 38 -
Rwork0.177 565 -
obs--25.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.87660.9166-0.05274.55280.0090.27320.0327-0.16070.17390.1491-0.01980.5025-0.0507-0.1044-0.0130.03820.01230.03070.1126-0.01150.128825.44132.851-0.044
23.486-1.2040.04215.3875-0.06231.88570.24730.34560.395-0.31420.1053-0.9681-0.3040.7028-0.35260.4567-0.10150.18680.7662-0.12410.354219.8697.45338.742
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A171 - 586
2X-RAY DIFFRACTION2B172 - 585

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