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- PDB-6awt: Structure of PR 10 Allergen in complex with epicatechin -

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Basic information

Entry
Database: PDB / ID: 6awt
TitleStructure of PR 10 Allergen in complex with epicatechin
ComponentsPR 10 protein
KeywordsPLANT PROTEIN / PEANUT / ALLERGEN
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 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 / BENZOIC 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. / Perdue, M. / 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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: PR 10 protein
B: PR 10 protein
C: PR 10 protein
D: PR 10 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,30114
Polymers67,3684
Non-polymers1,93310
Water2,162120
1
A: PR 10 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4464
Polymers16,8421
Non-polymers6043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PR 10 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1553
Polymers16,8421
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PR 10 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4464
Polymers16,8421
Non-polymers6043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PR 10 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2543
Polymers16,8421
Non-polymers4122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.451, 62.507, 186.585
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
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: 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
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
PR 10 protein


Mass: 16842.014 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arachis hypogaea (peanut) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6VT83*PLUS
#2: Chemical
ChemComp-28E / (2R,3R)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol / Epicatechin


Mass: 290.268 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H14O6
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 200 mM NaCl, 100 mM Bis-Tris pH 6.5, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 20, 2013
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: 29305 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.026 / Rrim(I) all: 0.071 / Rsym value: 0.05 / Net I/σ(I): 36.1
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1203 / Rpim(I) all: 0.281 / Rrim(I) all: 0.66 / Rsym value: 0.468 / % possible all: 83.3

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Processing

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

4map


Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT / ESU R: 0.399 / ESU R Free: 0.25 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25156 1447 4.9 %RANDOM
Rwork0.21502 ---
obs0.21683 27787 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 67.317 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2---2.2 Å20 Å2
3---1.74 Å2
Refinement stepCycle: 1 / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4688 0 138 120 4946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.024937
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7732.0246713
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3045622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74426.429182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86915819
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.302154
X-RAY DIFFRACTIONr_chiral_restr0.0930.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213697
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_it2.3913.6542497
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.8525.473116
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.154.1792440
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.10635.38219886
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)
11A3920.16
12B3920.16
21A3820.13
22C3820.13
31A4040.15
32D4040.15
41B3820.15
42C3820.15
51B4060.17
52D4060.17
61C3740.12
62D3740.12
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 92 -
Rwork0.293 1744 -
obs--85.75 %
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)
14.86210.38920.51680.628-1.158.0949-0.0172-0.31890.21560.1792-0.0005-0.2682-0.46150.92440.01770.20580.0075-0.05080.339-0.10570.21239.28711.30213.307
23.11950.16230.797410.03480.28652.45190.0248-0.2182-0.09180.4936-0.1237-0.0792-0.008-0.16770.09890.0847-0.02-0.00810.4763-0.03330.012920.76911.44612.991
33.78480.60660.70971.38690.76755.07780.10230.3277-0.00280.0440.013-0.15-0.35040.2524-0.11530.111-0.02510.01730.4001-0.04430.05333.210.4774.518
44.60676.6459-5.629612.4568-1.346625.3662-0.77630.31780.5534-0.97780.33631.08450.5945-1.14780.43990.33960.0039-0.21270.52050.0040.185732.67614.81921.61
56.2149-0.0272-0.36072.33060.33177.7872-0.45110.20030.5415-0.13850.0544-0.2487-0.47850.46820.39660.0831-0.0397-0.06280.39980.08460.115836.1430.12234.936
67.0677-2.5899-2.49653.64760.9377.255-0.4546-0.1245-0.3606-0.01180.1990.28510.3035-0.56860.25570.04670.01740.01910.54360.04760.033819.14723.1636.884
78.01561.0802-3.50991.7415-3.678112.1009-0.078-0.8070.24910.02710.0291-0.1086-0.2448-0.36010.04880.05750.0911-0.04480.5807-0.02570.077826.17930.53841.715
83.94630.32922.80681.79470.71029.3502-0.2046-0.2267-0.0691-0.01240.0516-0.0440.1781-0.20490.1530.02580.02910.01540.50130.05970.015532.96525.69538.589
92.6905-0.49971.13942.1927-0.41879.9868-0.0017-0.2175-0.03970.16410.2263-0.2816-0.0250.4911-0.22470.05690.0325-0.00220.4186-0.02660.055462.54240.98412.479
103.1837-0.6476-0.22221.03111.35581.96530.01450.0318-0.18890.0107-0.07330.0571-0.03410.02460.05890.1875-0.0452-0.00250.51680.06280.064750.94840.2449.565
113.71182.31112.10278.89644.618622.46580.03210.22850.4644-0.3988-0.3430.0918-1.5192-0.42210.31090.12280.06770.01390.48850.08450.075655.46248.414-4.012
1213.72365.1915-12.929210.12-4.063513.4197-0.02511.14831.26730.42561.29811.03750.4957-0.8422-1.27290.29420.02690.00350.81880.17280.185256.69844.90221.238
135.36580.21483.75182.0119-0.596814.3192-0.42590.16340.2474-0.18490.1749-0.1367-0.34070.39160.2510.0675-0.1126-0.00540.3955-0.02070.036363.09459.68332.64
143.5942-1.2705-3.30644.82071.987112.1534-0.40680.1163-0.0639-0.0042-0.1017-0.21520.5663-0.88070.50850.0583-0.01460.03090.6912-0.11930.071346.45355.49537.301
154.25060.4281-1.0212.4713-0.2029.2141-0.0875-0.49710.1991-0.0675-0.0228-0.02180.1402-0.07110.11040.0144-0.0182-0.00680.6413-0.04720.018660.30457.34742.362
1621.5226-0.754518.54963.49340.068917.0411-0.8181-0.3123-0.0484-0.14160.54450.0101-0.6636-0.32970.27360.2096-0.10440.01210.6764-0.00380.12656.01555.12324.016
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 22
2X-RAY DIFFRACTION2A23 - 66
3X-RAY DIFFRACTION3A67 - 134
4X-RAY DIFFRACTION4A135 - 157
5X-RAY DIFFRACTION5B2 - 21
6X-RAY DIFFRACTION6B22 - 70
7X-RAY DIFFRACTION7B71 - 91
8X-RAY DIFFRACTION8B92 - 157
9X-RAY DIFFRACTION9C2 - 23
10X-RAY DIFFRACTION10C24 - 117
11X-RAY DIFFRACTION11C118 - 136
12X-RAY DIFFRACTION12C137 - 157
13X-RAY DIFFRACTION13D2 - 22
14X-RAY DIFFRACTION14D23 - 73
15X-RAY DIFFRACTION15D74 - 138
16X-RAY DIFFRACTION16D139 - 157

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