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- PDB-4dsc: Complex structure of abscisic acid receptor PYL3 with (+)-ABA in ... -

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Basic information

Entry
Database: PDB / ID: 4dsc
TitleComplex structure of abscisic acid receptor PYL3 with (+)-ABA in spacegroup of H32 at 1.95A
ComponentsAbscisic acid receptor PYL3
KeywordsHORMONE RECEPTOR / abscisic acid receptor / ABA / pyl3
Function / homology
Function and homology information


protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / 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-A8S / Abscisic acid receptor PYL3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZhang, X. / Chen, Z.
CitationJournal: Structure / Year: 2012
Title: Complex Structures of the Abscisic Acid Receptor PYL3/RCAR13 Reveal a Unique Regulatory Mechanism
Authors: Zhang, X. / Zhang, Q. / Xin, Q. / Yu, L. / Wang, Z. / Wu, W. / Jiang, L. / Wang, G. / Tian, W. / Deng, Z. / Wang, Y. / Liu, Z. / Long, J. / Gong, Z. / Chen, Z.
History
DepositionFeb 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Abscisic acid receptor PYL3
B: Abscisic acid receptor PYL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0326
Polymers42,4542
Non-polymers5774
Water10,935607
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-36 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.836, 232.836, 53.292
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-485-

HOH

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Components

#1: Protein Abscisic acid receptor PYL3 / PYR1-like protein 3 / Regulatory components of ABA receptor 13


Mass: 21227.234 Da / Num. of mol.: 2 / Fragment: UNP residues 25-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g73000, PYL3 / Plasmid: pgex 4t-2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) cells / References: UniProt: Q9SSM7
#2: Chemical ChemComp-A8S / (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid / (+)-abscisic acid / (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexen-1-yl]-3-methyl-2,4-pentadienoic acid


Mass: 264.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H20O4 / Comment: hormone*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 3.27 Å3/Da / Density % sol: 62.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 1.6M (NH)2SO4, 0.1M HEPES, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 40074 / Num. obs: 39972 / % possible obs: 99.75 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.096
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.469 / Num. unique all: 1981 / % possible all: 4.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KLX

3klx


Resolution: 1.95→38.81 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.482 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21071 1997 5 %RANDOM
Rwork0.18484 37938 --
obs0.18616 37938 99.75 %-
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 max: 90.81 Å2 / Biso mean: 31.8795 Å2 / Biso min: 11.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å2-0 Å2
2--0.74 Å2-0 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 40 607 3300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022767
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9553783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2095355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69623.364107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62115427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1171517
X-RAY DIFFRACTIONr_chiral_restr0.2610.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212060
X-RAY DIFFRACTIONr_rigid_bond_restr3.43532767
X-RAY DIFFRACTIONr_sphericity_free25.2485117
X-RAY DIFFRACTIONr_sphericity_bonded14.22853208
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 139 -
Rwork0.22 2707 -
all-2846 -
obs--99.48 %
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)
14.441.4083-0.34522.8782-0.27280.1559-0.071-0.0429-0.30240.04210.068-0.2850.17840.00660.0030.27090.0347-0.0430.17840.01830.145747.8795-42.321927.146
20.64320.4024-0.05691.58750.39450.66690.0105-0.0041-0.0076-0.05640.0369-0.05820.00190.0309-0.04740.16850.0086-0.00870.16440.01390.150244.3166-32.081223.4816
30.4854-0.0643-0.69230.7204-0.10171.04750.0110.04580.02260.0150.01450.0853-0.0256-0.0825-0.02550.1505-0.0040.00230.16010.0020.159931.3923-24.616421.824
44.652.30691.391.14460.69571.0801-0.0943-0.01840.2955-0.0496-0.0090.1499-0.2198-0.03790.10330.2008-0.0017-0.00690.1706-0.01810.195125.5399-28.699733.6521
51.09170.29450.05160.6139-0.13171.37630.00140.0791-0.0131-0.05720.0330.05090.0952-0.1477-0.03440.1622-0.00240.00270.1684-0.00440.161726.3249-31.031218.0641
60.88280.51441.00130.3520.52211.7672-0.0056-0.0712-0.04080.0640.0021-0.0060.0382-0.05060.00350.175-0.00060.00470.18080.00150.171635.0929-34.572130.1503
73.59243.1093-8.49352.6932-7.351120.0935-0.89620.2071-0.5768-0.4916-0.1297-0.50241.3966-0.54591.02590.5438-0.09340.13570.5256-0.06470.569627.0981-39.912814.1347
80.5695-0.31390.09450.20510.06480.44510.04740.0280.0241-0.00480.0051-0.02980.1050.0876-0.05240.1723-0.00090.00610.18870.00640.172247.1239-31.78727.5018
91.10560.54350.57961.09650.64590.72230.03320.0102-0.10130.02250.0106-0.07780.09340.0581-0.04380.1651-0.0084-0.00310.1634-0.00540.160944.548-35.167922.0184
103.54282.43823.774210.16727.39297.4106-0.37170.4016-0.0766-1.02210.5120.2428-0.36690.2802-0.14020.5317-0.2961-0.16660.31360.02970.11537.4986-43.77817.5285
110.1222-0.6294-0.18393.45770.46431.69980.0083-0.00130.0008-0.06080.0203-0.07850.07430.0186-0.02860.1361-0.00270.00260.15280.00410.142842.2692-28.785415.8505
1210.15066.83712.23265.99253.54343.4952-0.19410.44371.1718-0.46910.56320.3658-0.54140.4498-0.3690.3154-0.03710.01990.20180.01150.338147.9589-14.757622.8547
130.7554-1.1138-0.06712.8138-0.32710.51720.0210.0030.06080.0247-0.0361-0.11870.00250.02840.0150.1639-0.00310.00090.17990.00840.167859.6928-22.9603-1.8351
140.79330.42330.26891.3504-0.14340.60560.0772-0.0558-0.04610.0461-0.0368-0.0770.0579-0.0258-0.04040.14630.00910.02080.17-0.00690.144249.7039-22.10142.1494
150.6013-0.5638-0.17630.9151-0.5211.54630.00090.01450.0470.01050.00190.0514-0.0402-0.1132-0.00290.1407-0.0096-0.00150.1508-0.00340.162836.8903-15.88624.3813
160.5621-0.1808-0.10670.96230.22960.90020.00920.01050.0229-0.04440.0036-0.0304-0.05990.0043-0.01280.1553-0.0036-0.00190.15080.00920.158341.9025-9.78960.5847
174.6333-1.8956-2.05721.92510.15861.3207-0.0144-0.30760.32730.11320.1006-0.243-0.06220.1665-0.08620.1962-0.0122-0.02660.2108-0.03040.190948.7173-5.254710.252
180.7227-0.0019-0.07450.6341-0.19960.3601-0.02410.0051-0.0352-0.073-0.008-0.10550.07660.07270.03210.1491-0.0001-0.00310.1611-0.00150.15951.7938-24.22530.6644
193.154.54730.88276.70880.76094.14150.1774-0.2933-0.01710.3107-0.2977-0.0432-0.05220.04440.12030.19110.0244-0.01680.2993-0.01640.156156.6234-11.783417.6437
202.53161.8180.94983.40161.11182.42820.0293-0.0108-0.1025-0.00780.0057-0.04320.0924-0.0476-0.0350.14060.0120.00930.13260.00620.135443.3862-25.50347.931
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 46
2X-RAY DIFFRACTION2A47 - 67
3X-RAY DIFFRACTION3A68 - 88
4X-RAY DIFFRACTION4A89 - 99
5X-RAY DIFFRACTION5A100 - 120
6X-RAY DIFFRACTION6A121 - 137
7X-RAY DIFFRACTION7A138 - 143
8X-RAY DIFFRACTION8A144 - 162
9X-RAY DIFFRACTION9A163 - 176
10X-RAY DIFFRACTION10A177 - 188
11X-RAY DIFFRACTION11A189 - 202
12X-RAY DIFFRACTION12A203 - 209
13X-RAY DIFFRACTION13B22 - 45
14X-RAY DIFFRACTION14B46 - 67
15X-RAY DIFFRACTION15B68 - 87
16X-RAY DIFFRACTION16B88 - 135
17X-RAY DIFFRACTION17B136 - 145
18X-RAY DIFFRACTION18B146 - 176
19X-RAY DIFFRACTION19B177 - 189
20X-RAY DIFFRACTION20B190 - 207

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