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- PDB-6v8j: Crystal structure of Ara h 8.0201 -

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Basic information

Entry
Database: PDB / ID: 6v8j
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
Ara h 8 allergen isoform
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsOffermann, L.R. / Pote, S. / Hurlburt, B.K. / McBride, J.K. / Chruszcz, M.
CitationJournal: To Be Published
Title: Crystal structure of Ara h 8.0201
Authors: Offermann, L.R. / Pote, S. / 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)66,59016
Polymers65,7304
Non-polymers86012
Water2,756153
1
A: Ara h 8 allergen isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7445
Polymers16,4321
Non-polymers3114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ara h 8 allergen isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5523
Polymers16,4321
Non-polymers1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ara h 8 allergen isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7445
Polymers16,4321
Non-polymers3114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ara h 8 allergen isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5523
Polymers16,4321
Non-polymers1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.406, 59.209, 67.078
Angle α, β, γ (deg.)89.960, 89.990, 71.020
Int Tables number1
Space group name H-MP1
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 9.5 / Details: 10 mM CHES/NaOH, 20%w/v PEG 8000, pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.365
11-h,-k,l20.253
11H, H-K, -L30.204
11-H, -H+K, -L40.177
ReflectionResolution: 1.95→40 Å / Num. obs: 39685 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.057 / Rrim(I) all: 0.084 / Rsym value: 0.062 / Net I/σ(I): 14.8
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1963 / CC1/2: 0.74 / CC star: 0.922 / Rpim(I) all: 0.348 / Rrim(I) all: 0.514 / Rsym value: 0.376 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MAP

4map


Resolution: 1.95→31.96 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.255 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.033
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED Discrepancy between R and Rfree factors most likely are caused by a different handling of twinning as discussed in ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED Discrepancy between R and Rfree factors most likely are caused by a different handling of twinning as discussed in the paper. The authors have used automatic way of handling the twinning as it is implemented in Refmac. Xtriage and Refmac define a different set of twinning operators and twining fractions
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 1965 5 %RANDOM
Rwork0.1728 ---
obs0.175 37683 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.65 Å2 / Biso mean: 29.103 Å2 / Biso min: 9.09 Å2
Baniso -1Baniso -2Baniso -3
1--4.15 Å21.32 Å2-0.75 Å2
2---3.1 Å23.06 Å2
3---7.26 Å2
Refinement stepCycle: final / Resolution: 1.95→31.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4524 0 44 153 4721
Biso mean--51.7 26.08 -
Num. residues----605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134639
X-RAY DIFFRACTIONr_bond_other_d0.0360.0174314
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.656301
X-RAY DIFFRACTIONr_angle_other_deg2.3541.58310098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8835599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89726.686172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58515781
X-RAY DIFFRACTIONr_chiral_restr0.0940.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025120
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02784
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A41820.13
12B41820.13
21A41950.14
22C41950.14
31A42060.12
32D42060.12
41B42390.11
42C42390.11
51B41800.12
52D41800.12
61C41400.13
62D41400.13
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.252 180 -
Rwork0.206 2601 -
obs--90.79 %
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)
12.7933-6.54361.397624.2142-2.86872.06630.1490.08540.0199-0.295-0.09910.3280.26050.1434-0.050.0959-0.05590.01920.0994-0.02940.03744.55-1.85113.75
20.06330.2317-0.11441.39250.29561.2488-0.022-0.01180.0228-0.14040.00220.03990.09450.0080.01990.1771-0.12120.06560.12920.0010.2327-2.659-0.256-4.773
31.477-2.9925-0.58468.70132.40140.7930.23070.1309-0.1757-0.5454-0.0844-0.1264-0.12670.0292-0.14640.1348-0.0157-0.01510.1921-0.13330.339910.114-12.5853.283
43.288-3.41281.01035.1313-2.3711.6440.02450.05270.0770.1258-0.09-0.01640.0858-0.05980.06550.2091-0.12230.05420.1122-0.04180.15372.319-0.5128.76
52.3493-3.1042.76936.8658-5.37224.32840.10890.03220.0604-0.2662-0.1795-0.09980.18770.13080.07070.1506-0.06960.050.0528-0.00350.15145.626.958-1.392
60.9489-1.5198-1.60296.11451.51053.7234-0.0467-0.082-0.05940.19410.04230.11630.13170.15280.00440.1141-0.12160.02650.1644-0.01090.197911.77419.8446.989
70.03240.11930.11983.1952-0.92581.25730.0263-0.0035-0.0109-0.3006-0.035-0.08230.13640.1290.00880.2514-0.13710.08590.1269-0.00550.191213.81528.332-8.743
81.5676-0.48211.78990.2159-0.15144.4378-0.0851-0.1494-0.0797-0.02710.07710.0313-0.3549-0.09460.0080.1992-0.13090.07450.1313-0.00420.250214.95231.085-2.311
90.7624-0.924-0.23923.70920.43270.78160.00790.0043-0.03970.03590.00090.0686-0.1459-0.0861-0.00880.158-0.08380.08750.139-0.00750.13477.70730.0396.184
103.07531.846-2.67645.3609-0.71312.5183-0.0214-0.13210.00180.0087-0.0110.11770.01560.13670.03240.1278-0.1010.03320.0892-0.01990.17779.01216.477-4.047
110.24050.011-0.30882.1217-0.72450.652-0.0017-0.02160.02250.1604-0.0268-0.0003-0.03930.0480.02860.1551-0.11480.08190.1287-0.0180.196114.0165.93336.288
123.05061.9385-2.19761.3116-1.09562.96910.1356-0.03810.00810.157-0.0799-0.04780.1251-0.1149-0.05580.2148-0.11390.03970.09790.01760.211412.667-1.83636.358
1312.98753.461-5.01891.3131-2.40095.88230.1401-0.01490.20430.0535-0.02280.12630.3659-0.2105-0.11720.391-0.15710.03960.0881-0.01150.09683.894-8.56329.136
142.82333.06980.20064.0191.09731.4446-0.0980.140.1352-0.09170.16780.14280.0917-0.0354-0.06980.1142-0.0870.02330.09210.01930.14477.9293.17124.84
151.87891.59452.08257.66781.60293.3805-0.0286-0.1084-0.01690.1568-0.05030.05830.20010.07270.07890.1916-0.06780.10390.146-0.02410.13147.85312.47236.797
160.31580.0893-0.08262.37270.94411.37420.0240.0248-0.02760.2636-0.02460.00880.1517-0.09180.00060.1849-0.10570.06830.0864-0.00240.1905-1.31126.34436.134
179.644-1.67696.48473.3237-1.18284.6507-0.00580.1426-0.48470.39390.1496-0.1717-0.08140.0313-0.14380.2461-0.04360.00810.1418-0.04380.21810.7838.21640.902
183.53593.00540.34293.28150.33161.61880.1547-0.1241-0.10620.1037-0.0836-0.0653-0.060.0589-0.0710.1409-0.09960.09390.1028-0.00990.1741-2.70633.86529.488
192.79244.3877-1.01677.6526-2.46451.6385-0.0165-0.0496-0.0119-0.1829-0.0289-0.04260.01310.08180.04530.1801-0.09370.08270.111-0.02230.15832.36629.34323.293
201.56771.5948-1.57485.603-4.16343.6720.10040.081-0.00850.4173-0.0466-0.0516-0.23520.1143-0.05380.1625-0.1010.03940.1572-0.03540.16636.78724.92633.684
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 9
2X-RAY DIFFRACTION2A10 - 90
3X-RAY DIFFRACTION3A91 - 96
4X-RAY DIFFRACTION4A97 - 131
5X-RAY DIFFRACTION5A132 - 153
6X-RAY DIFFRACTION6B2 - 19
7X-RAY DIFFRACTION7B20 - 60
8X-RAY DIFFRACTION8B61 - 79
9X-RAY DIFFRACTION9B80 - 138
10X-RAY DIFFRACTION10B139 - 153
11X-RAY DIFFRACTION11C2 - 53
12X-RAY DIFFRACTION12C54 - 90
13X-RAY DIFFRACTION13C91 - 98
14X-RAY DIFFRACTION14C99 - 136
15X-RAY DIFFRACTION15C137 - 153
16X-RAY DIFFRACTION16D2 - 45
17X-RAY DIFFRACTION17D46 - 69
18X-RAY DIFFRACTION18D70 - 104
19X-RAY DIFFRACTION19D105 - 128
20X-RAY DIFFRACTION20D129 - 153

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