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- PDB-6awv: Ara h 8.01 in complex with epicatechin -

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Basic information

Entry
Database: PDB / ID: 6awv
TitleAra h 8.01 in complex with epicatechin
ComponentsAra h 8 allergen
KeywordsPROTEIN BINDING / PLANT PROTEIN / PEANUT / ALLERGEN
Function / homology
Function and homology information


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
Chem-28E / BENZOIC ACID / Ara h 8 allergen
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsOffermann, L.R. / Perdue, M. / McBride, J. / Hurlburt, B.K. / Maleki, S.J. / Pote, S.S. / 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)51,85510
Polymers50,5263
Non-polymers1,3297
Water48627
1
A: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2543
Polymers16,8421
Non-polymers4122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1553
Polymers16,8421
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4464
Polymers16,8421
Non-polymers6043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)177.519, 52.232, 56.449
Angle α, β, γ (deg.)90.00, 96.87, 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: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLNGLNAA3 - 1562 - 155
21VALVALGLNGLNBB3 - 1562 - 155
12GLYGLYTYRTYRAA2 - 1571 - 156
22GLYGLYTYRTYRCC2 - 1571 - 156
13VALVALGLNGLNBB3 - 1562 - 155
23VALVALGLNGLNCC3 - 1562 - 155

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Ara h 8 allergen


Mass: 16842.014 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
#2: Chemical
ChemComp-28E / (2R,3R)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol / Epicatechin


Mass: 290.268 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H14O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200 mM magnesium chloride hexahydrate, 100 mM HEPES, pH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→40 Å / Num. obs: 16860 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.035 / Rrim(I) all: 0.071 / Rsym value: 0.046 / Net I/σ(I): 26.4
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 817 / Rpim(I) all: 0.324 / Rrim(I) all: 0.633 / Rsym value: 0.45 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MAP

4map


Resolution: 2.55→40 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / ESU R: 0.855 / ESU R Free: 0.324 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2622 820 4.9 %RANDOM
Rwork0.21896 ---
obs0.22115 16040 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 70.461 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å2-0 Å23.24 Å2
2---3.31 Å20 Å2
3---1.65 Å2
Refinement stepCycle: 1 / Resolution: 2.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 95 27 3610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023655
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7842.024973
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9935464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55326.444135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13215593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.953153
X-RAY DIFFRACTIONr_chiral_restr0.0870.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212747
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.2134.3991865
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.8076.5872326
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1714.7351790
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.82542.00514598
X-RAY DIFFRACTIONr_long_range_B_other
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)
11A3780.17
12B3780.17
21A3960.2
22C3960.2
31B3640.2
32C3640.2
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 46 -
Rwork0.354 1052 -
obs--89.12 %
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)
11.67570.4856-0.85221.6780.42581.73430.1110.0369-0.00560.0634-0.23070.23110.0503-0.27720.11980.17270.0020.13180.2577-0.0630.1451-20.556-3.9332.687
21.92231.0207-0.52323.57660.72454.25350.13860.15540.1562-0.1715-0.0419-0.1807-0.0571-0.2267-0.09660.13370.07410.10080.14130.00610.1361-14.8794.207-1.437
35.20174.6997-2.60587.9736-2.55712.33640.3637-0.04010.1005-0.347-0.4150.47680.26150.0310.05130.40880.02070.1110.3787-0.04310.2231-27.10.11510.765
42.95790.3259-0.96363.3126-1.29542.7447-0.02120.3088-0.2429-0.1382-0.2007-0.2431-0.11460.13510.22190.25960.02930.06550.2325-0.03590.06091.348-23.793-17.373
50.9342-0.7287-1.58133.06640.93972.7458-0.00640.1097-0.1274-0.0759-0.19770.1284-0.0398-0.11750.20420.21590.00740.0390.2271-0.05630.1048-4.904-22.117-10.924
69.03041.5584-5.10322-1.80643.4360.12450.19170.15390.0428-0.05590.157-0.1204-0.0667-0.06860.1632-0.0147-0.00610.2762-0.00290.1677-4.261-27.279-18.251
74.4419-0.3302-3.95513.26670.03524.6144-0.01540.7905-0.0881-0.12060.09960.0677-0.0428-0.853-0.08420.0472-0.0610.07640.434-0.08420.1502-43.558-1.70112.43
83.4941-0.3967-1.47143.52050.13072.1007-0.13010.5045-0.3450.28560.17230.7820.0295-0.682-0.04230.1445-0.04870.22670.46450.00360.4151-49.826-3.42219.864
93.9927-1.7759-2.60882.4942.49172.7605-0.03630.0819-0.06860.46740.04220.00390.41560.0529-0.00580.43990.00320.0790.4557-0.01670.278-37.9150.59311.243
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 66
2X-RAY DIFFRACTION2A67 - 137
3X-RAY DIFFRACTION3A138 - 157
4X-RAY DIFFRACTION4B3 - 41
5X-RAY DIFFRACTION5B42 - 120
6X-RAY DIFFRACTION6B121 - 157
7X-RAY DIFFRACTION7C2 - 43
8X-RAY DIFFRACTION8C44 - 133
9X-RAY DIFFRACTION9C134 - 157

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