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- PDB-6awy: Structure of peanut allergen Ara h 8.01. -

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Basic information

Entry
Database: PDB / ID: 6awy
TitleStructure of peanut allergen Ara h 8.01.
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
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOffermann, L.R. / Yarbrough, J. / 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0917
Polymers33,6842
Non-polymers4075
Water2,468137
1
A: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0343
Polymers16,8421
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0574
Polymers16,8421
Non-polymers2153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.858, 103.209, 49.292
Angle α, β, γ (deg.)90.00, 103.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / 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: 1 - 156

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

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Components

#1: Protein Ara h 8 allergen


Mass: 16842.014 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 0.2 M lithium sulfate, 34% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 20403 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.044 / Rrim(I) all: 0.086 / Rsym value: 0.063 / Net I/σ(I): 24.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1022 / Rpim(I) all: 0.31 / Rrim(I) all: 0.598 / Rsym value: 0.483 / % possible all: 99.9

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Processing

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

4map


Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.197 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 990 4.9 %RANDOM
Rwork0.20635 ---
obs0.20879 19340 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.344 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-0 Å20.83 Å2
2---2 Å2-0 Å2
3---0.58 Å2
Refinement stepCycle: 1 / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2354 0 21 137 2512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022414
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.61423271
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4455310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94526.44490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91915421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.539152
X-RAY DIFFRACTIONr_chiral_restr0.0960.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211772
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_it2.4593.6271246
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.8595.4261554
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3154.1671168
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.17234.6369693
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

Ens-ID: 1 / Number: 374 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 82 -
Rwork0.274 1403 -
obs--99.46 %
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)
10.521-0.7976-0.31514.33570.82651.38740.0637-0.057-0.1820.1121-0.06650.2234-0.02690.03370.00270.06660.00540.00190.1328-0.00570.10911.03-3.13221.623
20.54410.9260.33993.7452-1.27692.8124-0.08480.0268-0.0667-0.30990.25050.01040.1254-0.1356-0.16580.04520.01080.02090.1790.00990.04891.937-0.7683.012
35.3282-5.66913.13829.1485-3.43562.17950.07030.5523-0.01170.188-0.3544-0.2421-0.07820.28570.28420.09210.0659-0.09040.2339-0.02540.28126.063.65613.44
42.2221-3.99273.182710.9459-7.28545.79550.02760.1726-0.12310.3707-0.11850.167-0.17880.07760.09090.07840.0358-0.00320.1299-0.03940.1281-0.1312.03118.811
50.3142-0.8907-0.02164.56110.14131.19-0.0193-0.0259-0.0979-0.07520.11590.26990.0287-0.0597-0.09670.02560.0158-0.0130.1199-0.04390.1192-4.318-0.29214.299
60.3055-1.00610.56246.2044-0.48942.495-0.0917-0.03180.08610.5457-0.11380.1546-0.1178-0.05020.20550.0555-0.00790.03050.1387-0.01340.1488-10.953-25.85718.698
72.54291.47970.22516.96460.8040.3612-0.220.13440.1333-0.45560.2825-0.1081-0.03540.0457-0.06240.1079-0.03110.00640.1299-0.02010.028-3.567-29.1951.805
83.0022-2.6502-1.59867.9292.29991.0682-0.32510.1821-0.11720.37130.10660.59790.1825-0.00890.21850.05050.0170.01050.15090.04920.1292-9.769-31.90814.59
90.25851.1097-0.51136.0681-1.6821.2436-0.0345-0.0514-0.0738-0.0915-0.1008-0.46930.09290.13190.13530.05520.03020.00020.1260.03180.1612-1.637-31.90716.531
1022.5493-17.0792-2.960313.21212.18570.4123-0.4321-0.27730.13690.19480.4092-0.07360.081-0.00150.02290.1447-0.0763-0.05930.15060.02470.1994-14.626-4.1879.656
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 20
2X-RAY DIFFRACTION2A21 - 70
3X-RAY DIFFRACTION3A71 - 88
4X-RAY DIFFRACTION4A89 - 117
5X-RAY DIFFRACTION5A118 - 157
6X-RAY DIFFRACTION6B2 - 22
7X-RAY DIFFRACTION7B23 - 71
8X-RAY DIFFRACTION8B72 - 115
9X-RAY DIFFRACTION9B116 - 152
10X-RAY DIFFRACTION10B153 - 157

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