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- PDB-6aws: Structure of PR 10 Allergen Ara h 8.01 in complex with quercetin -

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Basic information

Entry
Database: PDB / ID: 6aws
TitleStructure of PR 10 Allergen Ara h 8.01 in complex with quercetin
ComponentsAra h 8 allergen
KeywordsPROTEIN BINDING / PLANT PROTEIN / PEANUT / ALLERGEN
Function / homology
Function and homology information


response to biotic stimulus / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
Pathogenesis-related proteins Bet v I family signature. / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3,5,7,3',4'-PENTAHYDROXYFLAVONE / Unknown ligand / Ara h 8 allergen
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsOffermann, L.R. / McBride, J. / Hurlburt, B.K. / Maleki, S.J. / Pote, S.S. / Perdue, M. / Chruszcz, M.
CitationJournal: To Be Published
Title: Structure of PR-10 Allergen Ara h 8.01.
Authors: Offermann, L.R. / Yarbrough, J. / McBride, J. / Hurlburt, B.K. / Maleki, S.J. / Pote, S.S. / Chruszcz, M.
History
DepositionSep 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Ara h 8 allergen
B: Ara h 8 allergen
C: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,83716
Polymers50,9203
Non-polymers1,91813
Water68538
1
A: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9038
Polymers16,9731
Non-polymers9307
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0323
Polymers16,9731
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9035
Polymers16,9731
Non-polymers9304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)181.568, 52.318, 57.497
Angle α, β, γ (deg.)90.00, 94.51, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 2 - 157 / Label seq-ID: 2 - 157

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Ara h 8 allergen


Mass: 16973.211 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arachis hypogaea (peanut) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6VT83

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Non-polymers , 5 types, 51 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H10O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 3 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris, pH 8.0, 200 mM Lithium sulfate, 34% PEG 4000
PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 22351 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.032 / Rrim(I) all: 0.065 / Rsym value: 0.048 / Net I/σ(I): 37.9
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1007 / Rpim(I) all: 0.293 / Rrim(I) all: 0.601 / Rsym value: 0.439 / % possible all: 88.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
MOLREPphasing
HKL-3000refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MAP

4map


Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.27 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26996 1177 5.3 %RANDOM
Rwork0.21779 ---
obs0.22047 21143 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 82.017 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å26.57 Å2
2---6.26 Å20 Å2
3---5 Å2
Refinement stepCycle: 1 / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 0 139 38 3629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023674
X-RAY DIFFRACTIONr_bond_other_d00.023324
X-RAY DIFFRACTIONr_angle_refined_deg1.5122.0315017
X-RAY DIFFRACTIONr_angle_other_deg3.74937733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8545467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23326.279129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07115571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.641153
X-RAY DIFFRACTIONr_chiral_restr0.0870.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214107
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02654
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_it2.6895.9391874
X-RAY DIFFRACTIONr_mcbond_other2.6875.9381873
X-RAY DIFFRACTIONr_mcangle_it4.3918.8982339
X-RAY DIFFRACTIONr_mcangle_other4.3918.8992340
X-RAY DIFFRACTIONr_scbond_it2.9986.511800
X-RAY DIFFRACTIONr_scbond_other2.9976.5141801
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0019.6612679
X-RAY DIFFRACTIONr_long_range_B_refined9.69972.8484228
X-RAY DIFFRACTIONr_long_range_B_other9.69872.8534229
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A82240.15
12B82240.15
21A83440.11
22C83440.11
31B80960.14
32C80960.14
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 77 -
Rwork0.372 1386 -
obs--87.71 %
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)
10.9908-0.4738-0.60062.2326-1.73274.27110.25240.07870.2111-0.1776-0.2564-0.1803-0.36590.11140.00410.22890.00010.13210.13730.03470.135617.66717.55321.55
22.94811.4994-0.17742.3577-0.43321.86890.066-0.0098-0.3925-0.0087-0.2158-0.36270.33420.07440.14980.2780.04870.06690.17690.06140.109918.848-0.24527.154
31.8438-0.32-0.70282.7151-0.27221.82650.0687-0.14380.08310.2278-0.03450.2024-0.04520.1652-0.03410.2687-0.03080.11580.15940.02880.074213.55212.81930.167
44.4495-1.1808-2.11423.83541.52741.28060.15060.179-0.0896-0.1125-0.1143-0.3428-0.0383-0.0684-0.03640.33020.08810.12040.24840.04640.116326.0327.92115.791
53.02441.0092-2.02392.60320.53362.0143-0.0482-0.1753-0.20260.1272-0.1045-0.05330.04560.09620.15270.3834-0.0489-0.08060.28970.0450.0374-2.908-15.31246.137
65.88791.3110.79661.69660.05093.69040.2874-0.39550.10430.2257-0.4398-0.078-0.122-0.06450.15230.3664-0.0814-0.0770.25620.04220.033.994-4.87341.065
72.46111.5952-1.4981.9381-0.30262.0883-0.4094-0.0722-0.5129-0.00360.084-0.50610.10220.03720.32540.36010.016-0.04020.25430.04050.23745.163-19.27939.893
88.8723-1.8551-2.67376.649-0.66881.05730.0243-0.1960.07250.05290.0098-0.00680.03530.0506-0.03410.2875-0.0196-0.07090.3666-0.04280.0316-7.553-16.33951.908
92.92051.0269-1.01144.0153-0.01152.3110.1167-0.8184-0.12540.3064-0.1563-0.4269-0.13560.42090.03950.10020.00940.06710.31590.02420.266543.5125.16615.917
103.97262.3408-0.05486.27283.21563.06850.001-0.2644-0.2841-0.03640.0016-0.59820.02490.4309-0.00250.09390.03580.12590.15810.11580.366546.468-0.12111.434
113.2475-0.8861-1.84760.69780.05862.58540.1977-0.69680.0692-0.15330.0544-0.3169-0.37630.6412-0.25210.2675-0.10560.29480.2822-0.03880.477548.03710.5657.68
123.483-0.2864-2.77732.35851.45025.28810.06580.04860.0334-0.1523-0.023-0.2584-0.0795-0.1994-0.04270.1668-0.01060.11460.1808-0.04280.228738.9887.859.398
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 20
2X-RAY DIFFRACTION2A21 - 64
3X-RAY DIFFRACTION3A65 - 140
4X-RAY DIFFRACTION4A141 - 157
5X-RAY DIFFRACTION5B2 - 40
6X-RAY DIFFRACTION6B41 - 75
7X-RAY DIFFRACTION7B76 - 139
8X-RAY DIFFRACTION8B140 - 157
9X-RAY DIFFRACTION9C2 - 52
10X-RAY DIFFRACTION10C53 - 87
11X-RAY DIFFRACTION11C88 - 121
12X-RAY DIFFRACTION12C122 - 157

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