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- PDB-3oqu: Crystal structure of native abscisic acid receptor PYL9 with ABA -

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Basic information

Entry
Database: PDB / ID: 3oqu
TitleCrystal structure of native abscisic acid receptor PYL9 with ABA
ComponentsAbscisic acid receptor PYL9
KeywordsHORMONE RECEPTOR / pyl9 / rcar1 / ABSCISIC ACID RECEPTOR
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / protein homodimerization activity / 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 PYL9
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsZhang, X. / Zhang, Q. / Chen, Z.
CitationJournal: Plos One / Year: 2013
Title: Structural Insights into the Abscisic Acid Stereospecificity by the ABA Receptors PYR/PYL/RCAR
Authors: Zhang, X. / Jiang, L. / Wang, G. / Yu, L. / Zhang, Q. / Xin, Q. / Wu, W. / Gong, Z. / Chen, Z.
History
DepositionSep 4, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Nov 1, 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 / 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 / _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 PYL9
B: Abscisic acid receptor PYL9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5454
Polymers46,0162
Non-polymers5292
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-10 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.024, 112.024, 40.433
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Abscisic acid receptor PYL9 / PYR1-like protein 9 / ABI1-binding protein 4 / Regulatory components of ABA receptor 1


Mass: 23008.111 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL9, RCAR1 / Plasmid: pet28b tev / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2(DE3) / References: UniProt: Q84MC7
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5
Details: 30% peg 4000, 0.1M tris, 0.2M li2So4, pH 8.5, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. all: 15887 / Num. obs: 15887 / % possible obs: 1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.084 / Rsym value: 0.069 / Net I/σ(I): 16
Reflection shellResolution: 2.68→2.73 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.31 / Num. unique all: 779 / Rsym value: 0.393 / % possible all: 95.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KLX

3klx


Resolution: 2.68→48.51 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 15.945 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R: 0.419 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20416 796 5 %RANDOM
Rwork0.1775 ---
obs0.17881 15081 99.51 %-
all-15113 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.194 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.68→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 38 231 2817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212643
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9763592
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6815329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2424.272103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58415450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6821516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211948
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_it0.431.51651
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81822683
X-RAY DIFFRACTIONr_scbond_it1.0283992
X-RAY DIFFRACTIONr_scangle_it1.794.5908
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.68→2.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 72 -
Rwork0.322 1071 -
obs--95.89 %
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)
1-11.0588-5.813813.0223-4.9432-6.483717.69340.07410.1063-0.17360.5681-0.6466-0.0734-0.59121.28720.57250.3569-0.114-0.05630.55450.01410.368514.86645.69710.616
22.83551.8889-1.78183.3475-0.38870.73920.0564-0.02550.1301-0.1516-0.0902-0.2683-0.04340.06720.03380.18650.0066-0.00680.20430.02540.22069.20349.599-3.729
32.9607-2.5976-2.04396.78021.68472.4189-0.08290.30090.4997-0.36150.05130.1135-0.0918-0.02910.03160.195-0.022-0.08020.14120.03220.283-4.21252.726-3.697
43.57462.43020.24554.18160.78851.4122-0.03-0.13430.07160.0636-0.11690.0368-0.15390.00920.14690.19480.02080.02750.1235-0.00190.13951.54451.5381.853
50.52872.4468-1.08464.197-3.44171.718-0.02630.0122-0.90630.181-0.2898-0.85020.25820.12470.31610.31810.02030.00840.2009-0.0830.41676.58946.341.633
62.57192.2937-0.57383.5537-0.6341.26220.0958-0.0890.08030.2312-0.0229-0.14960.22820.1059-0.07290.24180.01220.00180.1032-0.02380.15625.37838.0915.377
72.21750.2744-0.1964.4349-2.04374.1435-0.14590.7245-0.1911-0.58530.2929-0.23780.046-0.4351-0.14710.344-0.02910.07950.2433-0.01640.14649.61745.719-13.703
8-6.56720.8898-12.5969-3.88914.51232.2577-0.5055-0.0975-0.1761-0.4075-0.2261-0.2499-0.00610.92660.73150.40330.02780.07710.49080.14470.551914.47219.347-11.946
91.8117-1.52782.02082.317-0.28112.403-0.02110.14660.00570.2265-0.0239-0.21110.05770.17980.0450.2299-0.0117-0.03030.18340.01750.25059.60614.3053.794
103.4442.18130.72036.20571.00012.5016-0.0524-0.2655-0.48730.55860.04910.26820.1397-0.1010.00330.1898-0.02030.02760.10190.04150.2262-4.23512.1182.656
113.7479-1.70310.54192.842-0.22951.73930.02420.1872-0.02250.0363-0.10930.01520.2388-0.00420.08510.1636-0.0485-0.01470.1301-0.00780.14081.7112.992-2.77
12-1.4726-0.4661-0.40314.0175-3.64051.71230.00230.13360.3917-0.2195-0.4225-0.7345-0.2160.0460.42020.23780.0089-0.00570.15150.02210.43156.24118.184-3.226
131.445-1.0421.22842.5761-0.6242.6871-0.049-0.05840.00630.10070.0865-0.2582-0.2239-0.0151-0.03740.1994-0.0028-0.04410.1203-0.01620.17446.98723.6960.72
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 31
2X-RAY DIFFRACTION2A32 - 59
3X-RAY DIFFRACTION3A60 - 85
4X-RAY DIFFRACTION4A86 - 112
5X-RAY DIFFRACTION5A113 - 135
6X-RAY DIFFRACTION6A137 - 166
7X-RAY DIFFRACTION7A167 - 184
8X-RAY DIFFRACTION8B18 - 32
9X-RAY DIFFRACTION9B33 - 59
10X-RAY DIFFRACTION10B60 - 85
11X-RAY DIFFRACTION11B86 - 111
12X-RAY DIFFRACTION12B112 - 134
13X-RAY DIFFRACTION13B137 - 184

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