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- PDB-6ax0: Structure of PR-10 Allergen Ara h 8.01 in complex with epicatechin -

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Basic information

Entry
Database: PDB / ID: 6ax0
TitleStructure of PR-10 Allergen Ara h 8.01 in complex with epicatechin
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
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
Chem-28E / Ara h 8 allergen
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5736
Polymers33,9462
Non-polymers6274
Water46826
1
A: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2863
Polymers16,9731
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2863
Polymers16,9731
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.435, 92.068, 39.489
Angle α, β, γ (deg.)90.00, 91.79, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / 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: 0 / Auth seq-ID: 2 - 157 / Label seq-ID: 2 - 157

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

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Components

#1: Protein Ara h 8 allergen


Mass: 16973.211 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-28E / (2R,3R)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol / Epicatechin / Catechin


Mass: 290.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H14O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 150 mM potassium bromide, 30% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 26, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 9891 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.036 / Rrim(I) all: 0.074 / Rsym value: 0.063 / Net I/σ(I): 29.8
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 467 / Rpim(I) all: 0.205 / Rrim(I) all: 0.423 / Rsym value: 0.333 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
MOLREPphasing
HKL-3000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MAP

4map


Resolution: 2.5→46.03 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.893 / Cross valid method: THROUGHOUT / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26855 557 5.7 %RANDOM
Rwork0.22531 ---
obs0.22796 9231 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.601 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å2-0 Å2-1.72 Å2
2---2.79 Å2-0 Å2
3---1.63 Å2
Refinement stepCycle: 1 / Resolution: 2.5→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 44 26 2398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022418
X-RAY DIFFRACTIONr_bond_other_d00.022245
X-RAY DIFFRACTIONr_angle_refined_deg1.7142.0123289
X-RAY DIFFRACTIONr_angle_other_deg3.75435237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3655310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16626.40489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81315396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.821152
X-RAY DIFFRACTIONr_chiral_restr0.1010.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212686
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02424
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_it1.2943.4411246
X-RAY DIFFRACTIONr_mcbond_other1.2933.4391245
X-RAY DIFFRACTIONr_mcangle_it2.1235.1561554
X-RAY DIFFRACTIONr_mcangle_other2.1235.1581555
X-RAY DIFFRACTIONr_scbond_it1.3063.6841172
X-RAY DIFFRACTIONr_scbond_other1.3053.6871173
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1485.471736
X-RAY DIFFRACTIONr_long_range_B_refined4.37541.4182570
X-RAY DIFFRACTIONr_long_range_B_other4.37541.4362571
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9168 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 39 -
Rwork0.286 682 -
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)
10.9039-1.1774-0.24678.68611.01173.0722-0.165-0.17710.05560.4660.5798-0.20630.0046-0.0499-0.41480.04570.02980.00560.1782-0.0180.09144.7185.19715.98
23.829-1.2953-4.35916.57861.87977.8928-0.13540.033-0.7583-0.3816-0.2910.7022-0.19060.04690.42630.0754-0.02420.03920.1717-0.0070.266-3.06-3.4478.179
31.91980.23361.192410.90936.01886.0541-0.286-0.206-0.04360.78940.25260.18220.240.05650.03340.12810.04550.00890.14940.03260.01534.765-2.6520.147
41.67822.4810.29739.8546-0.89231.21990.01660.0124-0.1165-0.21830.0227-0.31790.1422-0.0906-0.03940.17210.0480.02260.1805-0.05890.082311.916-12.09614.642
57.3572-6.35141.945516.6898-1.50284.1263-0.0534-0.26330.03520.26580.1763-0.4289-0.28540.3318-0.1230.0804-0.0330.02430.1341-0.02840.03056.02813.35515.372
63.6743-1.13990.35538.59772.59590.9604-0.327-0.13950.17010.68610.8857-1.97480.15830.2881-0.55870.16820.0606-0.12190.3549-0.17090.544522.89223.3718.444
72.5858-1.976-3.59059.67851.11765.34690.21090.12540.0159-0.6068-0.05460.5424-0.2233-0.1587-0.15630.0508-0.0104-0.0210.11260.01690.06217.75126.776-1.123
86.4166-6.33771.459310.7431-0.14541.51350.0396-0.03220.1354-0.21660.2218-0.6811-0.01120.1493-0.26130.0155-0.03970.01290.2091-0.03930.208620.03529.5355.081
91.34541.38961.051710.6361-4.41394.1494-0.0446-0.04640.21830.3524-0.12230.1732-0.25270.09050.16680.08660.07120.05170.1903-0.03810.176214.36241.15912.62
103.14890.83790.31212.83865.54443.388-0.2334-0.3502-0.13280.15970.28140.04190.09610.2432-0.04790.02550.0390.02670.15870.01840.089714.88415.657.177
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 40
2X-RAY DIFFRACTION2A41 - 73
3X-RAY DIFFRACTION3A74 - 119
4X-RAY DIFFRACTION4A120 - 140
5X-RAY DIFFRACTION5A141 - 157
6X-RAY DIFFRACTION6B2 - 22
7X-RAY DIFFRACTION7B23 - 72
8X-RAY DIFFRACTION8B73 - 119
9X-RAY DIFFRACTION9B120 - 137
10X-RAY DIFFRACTION10B138 - 157

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