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- PDB-3ujl: Crystal structure of abscisic acid bound PYL2 in complex with typ... -

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Basic information

Entry
Database: PDB / ID: 3ujl
TitleCrystal structure of abscisic acid bound PYL2 in complex with type 2C protein phosphatase ABI2
Components
  • Abscisic acid receptor PYL2
  • Protein phosphatase 2C 77
KeywordsSIGNALING PROTEIN / PYL2 / abscisic receptor / ABI2 / protein phosphatase 2C / ABA signaling
Function / homology
Function and homology information


photoinhibition / regulation of stomatal opening / protein phosphatase inhibitor complex / response to abscisic acid / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / response to osmotic stress / protein phosphatase inhibitor activity / protein serine/threonine phosphatase activity ...photoinhibition / regulation of stomatal opening / protein phosphatase inhibitor complex / response to abscisic acid / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / response to osmotic stress / protein phosphatase inhibitor activity / protein serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / negative regulation of protein kinase activity / signaling receptor activity / response to heat / protein homodimerization activity / identical protein binding / nucleus / metal ion binding / 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 77 / Abscisic acid receptor PYL2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhou, X.E. / Soon, F.-F. / Ng, L.-M. / Kovach, A. / Tan, M.H.E. / Suino-Powell, K.M. / He, Y. / Xu, Y. / Brunzelle, J.S. / Li, J. ...Zhou, X.E. / Soon, F.-F. / Ng, L.-M. / Kovach, A. / Tan, M.H.E. / Suino-Powell, K.M. / He, Y. / Xu, Y. / Brunzelle, J.S. / Li, J. / Melcher, K. / Xu, H.E.
CitationJournal: Science / Year: 2012
Title: Molecular mimicry regulates ABA signaling by SnRK2 kinases and PP2C phosphatases.
Authors: Soon, F.F. / Ng, L.M. / Zhou, X.E. / West, G.M. / Kovach, A. / Tan, M.H. / Suino-Powell, K.M. / He, Y. / Xu, Y. / Chalmers, M.J. / Brunzelle, J.S. / Zhang, H. / Yang, H. / Jiang, H. / Li, J. ...Authors: Soon, F.F. / Ng, L.M. / Zhou, X.E. / West, G.M. / Kovach, A. / Tan, M.H. / Suino-Powell, K.M. / He, Y. / Xu, Y. / Chalmers, M.J. / Brunzelle, J.S. / Zhang, H. / Yang, H. / Jiang, H. / Li, J. / Yong, E.L. / Cutler, S. / Zhu, J.K. / Griffin, P.R. / Melcher, K. / Xu, H.E.
History
DepositionNov 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Source and taxonomy
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_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 PYL2
B: Protein phosphatase 2C 77
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0276
Polymers55,6892
Non-polymers3374
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-30 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.430, 98.587, 132.835
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Abscisic acid receptor PYL2 / PYR1-like protein 2 / Regulatory components of ABA receptor 14


Mass: 19905.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL2, RCAR14, At2g26040, T19L18.15 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O80992
#2: Protein Protein phosphatase 2C 77 / AtPP2C77 / Protein ABSCISIC ACID-INSENSITIVE 2 / Protein phosphatase 2C ABI2 / PP2C ABI2


Mass: 35783.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ABI2, At5g57050, MHM17.19 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O04719, protein-serine/threonine phosphatase
#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.61 Å3/Da / Density % sol: 65.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 0.1 M HEPES, 6% (w/v) PEG 8000, 10% (w/v) sucrose, pH 7.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2010
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 25223 / Num. obs: 23335 / % possible obs: 92.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 39.12 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 87.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.925 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7837 / SU ML: 0.36 / σ(F): 0 / Phase error: 27.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2481 1668 7.23 %
Rwork0.2225 --
all0.2244 25223 -
obs0.2244 23086 80.19 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.01 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso max: 250.64 Å2 / Biso mean: 56.5293 Å2 / Biso min: 14.36 Å2
Baniso -1Baniso -2Baniso -3
1--14.7782 Å20 Å2-0 Å2
2--32.6852 Å2-0 Å2
3----17.9069 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3544 0 22 86 3652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083635
X-RAY DIFFRACTIONf_angle_d1.4064925
X-RAY DIFFRACTIONf_chiral_restr0.188556
X-RAY DIFFRACTIONf_plane_restr0.007639
X-RAY DIFFRACTIONf_dihedral_angle_d15.7641351
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.56890.44341100.37591494160468
2.5689-2.65170.3421200.3131541166171
2.6517-2.74650.34931350.29511626176174
2.7465-2.85630.34211180.27851669178776
2.8563-2.98620.3151480.27941724187278
2.9862-3.14350.25471340.24411768190281
3.1435-3.34020.26271490.24391830197983
3.3402-3.59770.2681260.23621839196581
3.5977-3.9590.23141640.21171852201684
3.959-4.53020.19351450.17241927207286
4.5302-5.70110.21071680.1682005217388
5.7011-29.92760.20541510.20512143229490

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