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- PDB-3jrq: Crystal structure of (+)-ABA-bound PYL1 in complex with ABI1 -

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Basic information

Entry
Database: PDB / ID: 3jrq
TitleCrystal structure of (+)-ABA-bound PYL1 in complex with ABI1
Components
  • Protein phosphatase 2C 56
  • Putative uncharacterized protein At5g46790
KeywordsHYDROLASE/Hormone Receptor / Plant Hormone Receptor / Abscisic acid / PYL1 / ABI1 / type 2C protein phosphatase / Abscisic acid signaling pathway / Cell membrane / Hydrolase / Magnesium / Manganese / Membrane / Metal-binding / Nucleus / Protein phosphatase / HYDROLASE-Hormone Receptor COMPLEX
Function / homology
Function and homology information


regulation of abscisic acid-activated signaling pathway / negative regulation of abscisic acid-activated signaling pathway / protein phosphatase inhibitor complex / regulation of stomatal movement / response to abscisic acid / abscisic acid binding / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity ...regulation of abscisic acid-activated signaling pathway / negative regulation of abscisic acid-activated signaling pathway / protein phosphatase inhibitor complex / regulation of stomatal movement / response to abscisic acid / abscisic acid binding / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / myosin phosphatase activity / calmodulin-dependent protein phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / abscisic acid-activated signaling pathway / plastid / protein phosphatase inhibitor activity / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / phosphatase activity / phosphoprotein phosphatase activity / protein dephosphorylation / response to cold / defense response / kinase binding / signaling receptor activity / response to heat / protein kinase binding / protein homodimerization activity / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. ...PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / : / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A8S / Protein phosphatase 2C 56 / Abscisic acid receptor PYL1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMiyazono, K. / Miyakawa, T. / Sawano, Y. / Kubota, K. / Tanokura, M.
CitationJournal: Nature / Year: 2009
Title: Structural basis of abscisic acid signalling
Authors: Miyazono, K. / Miyakawa, T. / Sawano, Y. / Kubota, K. / Kang, H.J. / Asano, A. / Miyauchi, Y. / Takahashi, M. / Zhi, Y. / Fujita, Y. / Yoshida, T. / Kodaira, K. / Yamaguchi-Shinozaki, K. / Tanokura, M.
History
DepositionSep 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
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

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Assembly

Deposited unit
A: Protein phosphatase 2C 56
B: Putative uncharacterized protein At5g46790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5873
Polymers57,3232
Non-polymers2641
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-10 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.010, 60.620, 84.960
Angle α, β, γ (deg.)90.00, 104.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein phosphatase 2C 56 / AtPP2C56 / Protein phosphatase 2C ABI1 / PP2C ABI1 / Protein ABSCISIC ACID-INSENSITIVE 1


Mass: 35875.992 Da / Num. of mol.: 1 / Fragment: UNP residues 125-429
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ABI1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: P49597, protein-serine/threonine phosphatase
#2: Protein Putative uncharacterized protein At5g46790 / PYL1


Mass: 21446.926 Da / Num. of mol.: 1 / Fragment: UNP residues 28-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VZS8
#3: 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.: 1 / Source method: obtained synthetically / Formula: C15H20O4 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 21% PEG3000, 0.1 M sodium citrate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 26472 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 45.868 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 10.88
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.150.3482.442641621178.1
2.15-2.210.292.945431708183.3
2.21-2.280.2643.245301657184.9
2.28-2.350.363.762561737188.9
2.35-2.420.3174.779041732193.4
2.42-2.510.3155.588651714195.9
2.51-2.60.286.290901654194.8
2.6-2.710.2377.691231612196.3
2.71-2.830.1998.988531555197.8
2.83-2.970.16510.987031492196.9
2.97-3.130.13613.285031439197.4
3.13-3.320.11916.281331360198.6
3.32-3.550.0991978401306199.2
3.55-3.830.09720.673151207199.4
3.83-4.20.08721.967531104198.7
4.2-4.70.0723.663411020199.4
4.7-5.420.06923.55661903199.8
5.42-6.640.07922.64857765199.2
6.64-9.390.06223.23701596199.3
9.39-200.0521.31597290182.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefmac_5.5.0088refinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A6Q and 3JRS

1a6q

3jrs


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.402 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1326 5 %RANDOM
Rwork0.198 ---
obs0.201 26467 93.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.84 Å2 / Biso mean: 30.132 Å2 / Biso min: 8.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.03 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 19 107 3619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223576
X-RAY DIFFRACTIONr_angle_refined_deg2.1691.9594838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3835439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.35423.095168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.75515617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7221536
X-RAY DIFFRACTIONr_chiral_restr0.160.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212704
X-RAY DIFFRACTIONr_mcbond_it1.1751.52207
X-RAY DIFFRACTIONr_mcangle_it2.09923565
X-RAY DIFFRACTIONr_scbond_it3.42531369
X-RAY DIFFRACTIONr_scangle_it5.344.51273
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 80 -
Rwork0.293 1541 -
all-1621 -
obs--78.2 %
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)
11.31-0.2158-0.28823.37561.71743.13480.015-0.03020.09470.040.0108-0.2085-0.20910.1064-0.02580.0879-0.046-0.00610.08090.00520.0227-5.2265-8.555328.941
21.61040.28760.3031.20720.45081.66560.00690.00090.0042-0.04540.0250.0252-0.00310.1241-0.03190.00760.00340.00080.0821-0.01840.1125-13.9624-30.3365-1.0708
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A125 - 423
2X-RAY DIFFRACTION2B32 - 210
3X-RAY DIFFRACTION2B1

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