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- PDB-6aww: Structure of PR 10 Allergen Ara h 8.01 in complex with 3-Hydroxy-... -

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Basic information

Entry
Database: PDB / ID: 6aww
TitleStructure of PR 10 Allergen Ara h 8.01 in complex with 3-Hydroxy-2-naphthoic acid
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
3-hydroxynaphthalene-2-carboxylic acid / Ara h 8 allergen
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 ...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
D: Ara h 8 allergen
E: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,20720
Polymers84,2105
Non-polymers1,99715
Water3,747208
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)17,4305
Polymers16,8421
Non-polymers5884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4305
Polymers16,8421
Non-polymers5884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2414
Polymers16,8421
Non-polymers3993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2414
Polymers16,8421
Non-polymers3993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.567, 130.513, 140.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: _ / 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-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15BB
25CC
16BB
26DD
17BB
27EE
18CC
28DD
19CC
29EE
110DD
210EE

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Ara h 8 allergen


Mass: 16842.014 Da / Num. of mol.: 5
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.: 5 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-BZJ / 3-hydroxynaphthalene-2-carboxylic acid


Mass: 188.179 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C11H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris, 25% PEG 3350, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 37595 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.018 / Rrim(I) all: 0.051 / Rsym value: 0.043 / Net I/σ(I): 45.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 4.75 / Num. unique obs: 1873 / Rpim(I) all: 0.155 / Rrim(I) all: 0.445 / Rsym value: 0.314 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
MOLREPphasing
HKL-3000refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MAP

4map


Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / ESU R: 0.399 / ESU R Free: 0.254 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25995 1900 5.1 %RANDOM
Rwork0.22521 ---
obs0.22698 35532 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.225 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å20 Å2-0 Å2
2---2.21 Å20 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5825 0 145 208 6178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.026083
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7142.0178256
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1525771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55226.502223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05151012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.192154
X-RAY DIFFRACTIONr_chiral_restr0.0920.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214567
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_it2.2763.6593102
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.7275.4793867
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.363.9282981
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.89334.90224792
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)
11A3700.15
12B3700.15
21A3580.17
22C3580.17
31A3540.17
32D3540.17
41A3600.19
42E3600.19
51B3560.14
52C3560.14
61B3740.16
62D3740.16
71B3680.16
72E3680.16
81C3560.16
82D3560.16
91C3600.2
92E3600.2
101D3600.19
102E3600.19
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 148 -
Rwork0.295 2579 -
obs--100 %
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)
11.3244-1.1233-0.74422.38510.49653.4417-0.09110.1236-0.24360.05020.09650.40850.3362-0.1391-0.00540.0939-0.07530.00160.1237-0.00890.0881-30.41512.50517.956
21.6329-2.2161-2.05123.67753.79354.8901-0.1958-0.1243-0.16110.10210.12850.28430.13850.36670.06730.2124-0.0539-0.070.2502-0.01250.1354-26.70218.82816.959
31.7556-0.6669-0.98931.9021-0.09722.5318-0.0983-0.00670.1445-0.0610.05330.05220.49730.06060.0450.2367-0.0047-0.04440.1369-0.06250.1139-9.0833.672-3.527
41.72280.13630.0281.72130.51275.5320.01420.0960.3043-0.00390.1050.30690.2612-0.124-0.11930.1285-0.0339-0.07030.06350.0220.1651-14.0699.548-7.75
52.4795-1.27932.00552.8685-0.75363.09070.36980.0035-0.1582-0.1049-0.23920.14330.3123-0.4758-0.13050.0729-0.0475-0.03550.31320.00010.0503-25.06520.711-26.304
65.63310.78213.24951.27030.91883.25920.0142-0.0824-0.18-0.184-0.0335-0.0207-0.0492-0.18580.01940.0352-0.0189-0.00380.14410.00860.0219-22.34526.753-30.923
72.45870.3606-0.55615.2761-0.57371.7174-0.03970.0066-0.02950.63220.0379-0.38370.07030.20880.00170.46490.0012-0.07590.1065-0.05910.06687.061-18.291-20.168
84.60921.3363-2.73722.4606-2.15676.5725-0.22520.10860.03970.55610.1907-0.3013-0.26510.24420.03440.51230.0395-0.06020.0802-0.0720.1055.351-9.539-17.796
93.4524-0.63920.42184.3778-2.05974.16420.2613-0.11660.1265-0.31310.05230.2170.1825-0.2934-0.31370.205-0.0430.02410.06310.03010.0517-29.414-19.08715.015
106.5416-2.6158-1.0842.23120.38153.8860.4421-0.02240.286-0.5004-0.0568-0.04860.2596-0.1652-0.38520.3522-0.08450.03660.08280.04110.1583-25.057-25.21416.276
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 114
2X-RAY DIFFRACTION2A115 - 157
3X-RAY DIFFRACTION3B2 - 94
4X-RAY DIFFRACTION4B95 - 157
5X-RAY DIFFRACTION5C2 - 105
6X-RAY DIFFRACTION6C106 - 157
7X-RAY DIFFRACTION7D2 - 101
8X-RAY DIFFRACTION8D102 - 157
9X-RAY DIFFRACTION9E2 - 85
10X-RAY DIFFRACTION10E86 - 157

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