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- PDB-3s7e: Crystal structure of Ara h 1 -

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Basic information

Entry
Database: PDB / ID: 3s7e
TitleCrystal structure of Ara h 1
ComponentsAllergen Ara h 1, clone P41B
KeywordsALLERGEN / bicupin / vicilin / seed storage 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 / MOLECULAR REPLACEMENT / Resolution: 2.71 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
Water50428
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_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area15640 Å2
ΔGint-129 kcal/mol
Surface area40310 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_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area15240 Å2
ΔGint-129 kcal/mol
Surface area40450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.368, 93.368, 237.111
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:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 2 / Auth seq-ID: 172 - 585 / Label seq-ID: 4 - 417

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


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.: 28 / 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: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG400, 100 mM NaCl, Na citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5718 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Jan 25, 2011 / Details: mirrors (VariMax)
RadiationMonochromator: VariMax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5718 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.761
11-H-K, K, -L20.239
ReflectionResolution: 2.7→50 Å / Num. all: 19169 / Num. obs: 19169 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 18.5
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 6.6 / Num. unique all: 680 / Rsym value: 0.159 / % possible all: 64.8

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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: PDB ENTRY 2EA7

2ea7


Resolution: 2.71→25.69 Å / Cor.coef. Fo:Fc: 0.76 / Cor.coef. Fo:Fc free: 0.717 / SU B: 36.192 / SU ML: 0.355 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOW VALUES OF THE CORRELATION COEFFICIENTS ARE MOST LIKELY CAUSED BY POOR QUALITY OF THE CRYSTAL USED FOR THE EXPERIMENT. DIFFRACTION DATA ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOW VALUES OF THE CORRELATION COEFFICIENTS ARE MOST LIKELY CAUSED BY POOR QUALITY OF THE CRYSTAL USED FOR THE EXPERIMENT. DIFFRACTION DATA FROM THIS CRYSTAL ARE HIGHLY ANISOTROPIC.
RfactorNum. reflection% reflectionSelection details
Rfree0.25968 834 5 %RANDOM
Rwork0.23646 ---
all0.2376 15974 --
obs0.2376 15974 80.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.248 Å2
Baniso -1Baniso -2Baniso -3
1--4.62 Å20 Å20 Å2
2---4.62 Å20 Å2
3---9.23 Å2
Refinement stepCycle: LAST / Resolution: 2.71→25.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5676 0 2 28 5706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225774
X-RAY DIFFRACTIONr_bond_other_d00.023875
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.9447810
X-RAY DIFFRACTIONr_angle_other_deg4.29939441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0345724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7724.884301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.70115961
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8071540
X-RAY DIFFRACTIONr_chiral_restr0.0810.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216554
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021146
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_it0.5411.53641
X-RAY DIFFRACTIONr_mcbond_other01.51473
X-RAY DIFFRACTIONr_mcangle_it0.83625834
X-RAY DIFFRACTIONr_scbond_it0.65932133
X-RAY DIFFRACTIONr_scangle_it1.1364.51976
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A2117tight positional0.030.05
A2475medium positional0.10.5
B2117tight thermal0.030.5
B2475medium thermal0.612
LS refinement shellResolution: 2.71→2.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 48 -
Rwork0.296 707 -
obs--48.55 %
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)
11.672-0.47860.08581.94370.06730.02280.0068-0.03660.34620.0534-0.0133-0.3077-0.01760.04480.00650.1857-0.0119-0.00550.1934-0.00710.095815.73515.53-0.166
22.2986-0.1048-0.12431.00310.11310.1290.01480.0721-0.2984-0.01850.03680.0170.10730.0268-0.05160.2388-0.0048-0.04660.191-0.01050.1559-2.78832.02238.602
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A171 - 586
2X-RAY DIFFRACTION2B171 - 586

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