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- PDB-6v8l: Crystal structure of Ara h 8.0201 -

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Basic information

Entry
Database: PDB / ID: 6v8l
TitleCrystal structure of Ara h 8.0201
ComponentsAra h 8 allergen isoform
KeywordsALLERGEN / peanut / PR-10
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-like domain superfamily
Similarity search - Domain/homology
icosanoic acid / Ara h 8 allergen isoform
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPote, S. / Offermann, L.R. / Hurlburt, B.K. / McBride, J.K. / Chruszcz, M.
CitationJournal: To Be Published
Title: Crystal structure of Ara h 8.0201
Authors: Pote, S. / Offermann, L.R. / Hurlburt, B.K. / McBride, J.K. / Chruszcz, M.
History
DepositionDec 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 isoform
B: Ara h 8 allergen isoform
C: Ara h 8 allergen isoform
D: Ara h 8 allergen isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4279
Polymers65,7304
Non-polymers6975
Water4,630257
1
A: Ara h 8 allergen isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5292
Polymers16,4321
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ara h 8 allergen isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5292
Polymers16,4321
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ara h 8 allergen isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6253
Polymers16,4321
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ara h 8 allergen isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7452
Polymers16,4321
Non-polymers3131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.913, 110.565, 65.772
Angle α, β, γ (deg.)90.000, 96.580, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 2 - 153 / Label seq-ID: 2 - 153

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Ara h 8 allergen isoform


Mass: 16432.467 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arachis hypogaea (peanut) / Gene: Ahy_Scaffold6g108211 / Plasmid: pET9a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B0YIU5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-DCR / icosanoic acid


Mass: 312.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H40O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: 0.1M HEPES, 2.4M Ammonium Sulfate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 40882 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.026 / Rrim(I) all: 0.047 / Rsym value: 0.039 / Net I/σ(I): 35.4
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2067 / CC1/2: 0.866 / CC star: 0.963 / Rpim(I) all: 0.234 / Rrim(I) all: 0.424 / Rsym value: 0.352 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6V8H

6v8h


Resolution: 1.95→24.1 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.403 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.18
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 1988 4.9 %RANDOM
Rwork0.218 ---
obs0.2201 38798 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 135.29 Å2 / Biso mean: 56.433 Å2 / Biso min: 30.54 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å2-0 Å21.51 Å2
2---2.1 Å20 Å2
3---0.72 Å2
Refinement stepCycle: final / Resolution: 1.95→24.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4460 0 28 257 4745
Biso mean--86.38 55.92 -
Num. residues----598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0134569
X-RAY DIFFRACTIONr_bond_other_d0.0360.0174245
X-RAY DIFFRACTIONr_angle_refined_deg1.521.6496210
X-RAY DIFFRACTIONr_angle_other_deg2.31.589916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43226.429168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0315749
X-RAY DIFFRACTIONr_chiral_restr0.0870.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025068
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02792
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A41160.09
12B41160.09
21A43200.07
22C43200.07
31A42680.09
32D42680.09
41B43070.1
42C43070.1
51B43610.08
52D43610.08
61C44900.09
62D44900.09
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 133 -
Rwork0.297 2897 -
all-3030 -
obs--99.7 %
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)
14.19343.126-1.863518.2834-5.84413.36720.06610.3463-0.2817-0.41150.44571.60880.0114-0.2706-0.51180.02030.0036-0.04840.12760.03320.24791.30347.789.129
23.78824.53635.896111.02012.401413.14370.6860.0796-0.35431.64740.35010.06220.47570.058-1.03621.06760.0170.02220.55130.02610.25616.07149.61324.861
32.4281.5641.755119.26350.0513.46740.0197-0.39490.162.93220.40662.019-0.4257-0.1862-0.42630.51230.10910.36880.32850.08130.33680.06959.44917.746
43.63731.0866-0.441417.4091-3.68851.4144-0.01670.164-0.15990.03520.1216-0.48420.0156-0.0909-0.10490.00160.0069-0.00890.1526-0.00520.09417.96954.1989.586
50.8186-1.75010.719615.2241-5.93633.285-0.04860.08550.04010.4793-0.1069-0.3651-0.17110.09190.15550.0817-0.0126-0.07030.1878-0.02570.09020.02531.30458.8
63.0442-2.40380.50199.0869-0.24663.47690.35110.5101-0.3625-1.89010.07681.120.48970.0171-0.42780.4803-0.0445-0.29040.4115-0.06170.2004-5.31126.54842.424
719.306-11.9641-16.270320.7165-6.420534.20730.46221.3794-0.1211-0.1656-1.4404-0.6908-0.5585-0.42610.97810.1560.09150.00650.2853-0.10410.36727.44915.15651.754
81.6076-0.1261-0.12029.4118-2.22262.71810.04010.1683-0.1813-0.4720.0295-0.16090.0870.1033-0.06970.0806-0.0126-0.04130.2283-0.04130.0730.84229.25152.119
94.2672-1.9019-0.048914.6325-0.84411.7948-0.19160.02740.77120.88060.2276-0.9165-0.21060.0252-0.0360.07420.0205-0.07250.15630.05120.25216.98735.27214.358
1012.4801-4.9336-5.63887.28422.14673.9892-0.29360.0260.04651.69490.2838-0.35060.0348-0.00510.00980.60540.1444-0.10750.24030.03440.037314.90723.99224.94
116.77421.9296-3.660414.8943-2.14134.3952-0.1052-0.39470.28310.69840.0964-1.38430.18980.25310.00880.07050.0075-0.10.23980.02770.210120.81824.92814.37
122.7877-1.50.435715.63261.24930.8508-0.08570.32410.2447-0.2968-0.08640.5636-0.0459-0.07110.17220.0369-0.0241-0.06270.19760.06840.12711.68128.51510.046
131.7856-5.2162-0.935127.19127.59442.6124-0.0133-0.0673-0.02760.35970.0228-0.17680.0495-0.0898-0.00950.17090.01950.02750.22410.050.14974.39954.95860.397
140.14870.42730.54897.6148-1.05763.4115-0.17820.0017-0.0905-1.33690.2153-0.702-0.1644-0.001-0.03710.3705-0.04230.19680.31130.02960.157710.42155.41342.15
152.5782-2.5125-0.735512.19411.9911.5552-0.0219-0.0345-0.01130.05550.05210.0833-0.1038-0.0835-0.03020.040.02030.01240.21850.06970.02364.94757.03755.26
164.589-5.2594-3.287813.25275.9024.3423-0.22050.05680.1474-0.56440.11430.12660.1459-0.01360.10620.2147-0.0290.00560.20180.04380.0443.52647.29944.838
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 26
2X-RAY DIFFRACTION2A27 - 41
3X-RAY DIFFRACTION3A42 - 92
4X-RAY DIFFRACTION4A93 - 153
5X-RAY DIFFRACTION5B2 - 13
6X-RAY DIFFRACTION6B14 - 86
7X-RAY DIFFRACTION7B91 - 94
8X-RAY DIFFRACTION8B95 - 153
9X-RAY DIFFRACTION9C2 - 37
10X-RAY DIFFRACTION10C38 - 69
11X-RAY DIFFRACTION11C70 - 91
12X-RAY DIFFRACTION12C92 - 153
13X-RAY DIFFRACTION13D2 - 10
14X-RAY DIFFRACTION14D11 - 91
15X-RAY DIFFRACTION15D92 - 132
16X-RAY DIFFRACTION16D133 - 153

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