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- PDB-6awz: Structure of PR-10 allergen from peanut (Ara h 8.01). -

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Basic information

Entry
Database: PDB / ID: 6awz
TitleStructure of PR-10 allergen from peanut (Ara h 8.01).
ComponentsAra h 8 allergen
KeywordsPLANT 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 / Resolution: 1.9 Å
AuthorsOffermann, L.R. / Majorek, K. / 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 1.1Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)33,9245
Polymers33,6842
Non-polymers2403
Water3,045169
1
A: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8652
Polymers16,8421
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0593
Polymers16,8421
Non-polymers2172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.869, 91.096, 55.079
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20 % PEG 8000, 0.1 M Tris-HCl pH 8.5, 0.1 M MgCl2, 20 % PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 23619 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.023 / Rrim(I) all: 0.057 / Rsym value: 0.043 / Net I/σ(I): 41.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1090 / Rpim(I) all: 0.223 / Rrim(I) all: 0.566 / Rsym value: 0.379 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOLREPphasing
HKL-2000data scaling
HKL-2000refinement
RefinementResolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25649 1218 5.2 %RANDOM
Rwork0.21389 ---
obs0.21603 22375 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.501 Å2
Baniso -1Baniso -2Baniso -3
1-6.49 Å20 Å20 Å2
2---4.32 Å2-0 Å2
3----2.16 Å2
Refinement stepCycle: 1 / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 15 169 2554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022426
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.721.9983279
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65326.59694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20615428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.761152
X-RAY DIFFRACTIONr_chiral_restr0.0910.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211792
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_it2.1963.311246
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.5664.9481554
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5543.6251180
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.44229.2993661
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: 386 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 105 -
Rwork0.349 1416 -
obs--87.31 %
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)
10.72771.6102-0.885411.1174-4.26366.03160.0647-0.19510.14360.4774-0.00080.48930.2682-0.0113-0.06390.1090.04550.03670.31-0.0120.108-9.79832.533-44.698
24.9021-0.8701-1.392410.26521.24845.23740.05940.19350.3633-1.65520.27030.18560.1707-0.3893-0.32980.3612-0.0122-0.05020.1660.03340.049-5.97339.716-60.482
38.45085.23640.461610.83190.412.2290.4025-0.3263-0.2038-2.43-0.19350.19640.7815-0.0768-0.2091.2764-0.0537-0.18750.280.00120.0433-6.56328.626-65.424
44.2382-3.5086-4.109611.38895.54527.7894-0.38330.0987-0.0557-0.57740.13230.63950.8555-0.19650.25110.3556-0.036-0.05770.26010.04480.0505-9.52225.756-55.619
51.8442-3.1363-1.775111.60910.67823.6942-0.24470.0465-0.07950.87440.09630.73520.6881-0.29520.14840.46-0.04930.17530.2951-0.02450.1878-11.07628.943-46.392
66.6387-2.78990.936213.797-1.54552.8673-0.1338-0.4046-0.1402-0.52180.0078-0.45220.37370.340.12590.32750.15340.12380.3670.04420.25292.12319.722-47.863
72.0744-3.85081.091412.672-3.14892.5554-0.1789-0.19050.0095-0.2990.11070.21030.0413-0.10630.06810.22330.02160.00850.32050.01070.3001-5.37341.279-52.559
80.5158-1.38621.29855.8917-3.41353.67070.26990.1555-0.014-0.8366-0.1820.0920.5910.145-0.08780.27720.03390.04360.3074-0.00810.1134-7.63813.318-38.47
93.8771-0.07931.25347.25910.84085.0687-0.0352-0.1389-0.2143-0.14880.2810.0327-0.0205-0.3454-0.24580.0560.01250.0140.20340.02150.136-7.6014.899-23.076
1016.2098-1.49879.08599.4714-1.70567.53550.1668-0.7327-0.27651.0116-0.00180.5987-0.166-0.8072-0.16510.25860.07270.19130.32650.04590.2101-16.02516.126-15.597
1111.6412-2.65925.91488.5977-1.6534.8608-0.3890.3064-0.15791.44790.5712-0.3783-0.79420.096-0.18210.42030.0613-0.01590.3043-0.06580.048-4.78217.325-18.088
121.13460.63861.49688.80040.52925.3232-0.1205-0.08520.063-0.0320.06580.556-0.1568-0.15580.05470.0540.03270.04170.32780.01890.1261-10.34617.136-29.527
131.61332.0191.278316.40932.24463.241-0.09930.05410.0655-0.56550.03910.44120.05710.09110.06020.19740.02060.01390.30020.0210.097-8.31517.78-36.37
140.97641.63210.234311.9533-2.80931.9562-0.03390.0775-0.1337-0.5871-0.0405-0.52810.29580.13810.07430.0810.01160.06150.23880.00590.2051-2.32610.243-31.084
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 17
2X-RAY DIFFRACTION2A18 - 41
3X-RAY DIFFRACTION3A42 - 73
4X-RAY DIFFRACTION4A74 - 101
5X-RAY DIFFRACTION5A102 - 125
6X-RAY DIFFRACTION6A126 - 135
7X-RAY DIFFRACTION7A136 - 157
8X-RAY DIFFRACTION8B2 - 15
9X-RAY DIFFRACTION9B16 - 40
10X-RAY DIFFRACTION10B41 - 50
11X-RAY DIFFRACTION11B51 - 73
12X-RAY DIFFRACTION12B74 - 106
13X-RAY DIFFRACTION13B107 - 125
14X-RAY DIFFRACTION14B126 - 157

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