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- PDB-3nmv: Crystal structure of pyrabactin-bound abscisic acid receptor PYL2... -

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Basic information

Entry
Database: PDB / ID: 3nmv
TitleCrystal structure of pyrabactin-bound abscisic acid receptor PYL2 mutant A93F in complex with type 2C protein phosphatase ABI2
Components
  • Abscisic acid receptor PYL2
  • Protein phosphatase 2C 77
KeywordsPROTEIN BINDING / PYL2 / Pyrabactin / Abscisic acid receptor / helix-grip fold / type 2C protein phosphatase
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 ...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 / protein serine/threonine phosphatase activity / negative regulation of protein kinase activity / signaling receptor activity / response to heat / 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-PYV / Protein phosphatase 2C 77 / Abscisic acid receptor PYL2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhou, X.E. / Melcher, K. / Ng, L.-M. / Soon, F.-F. / Xu, Y. / Suino-Powell, K.M. / Kovach, A. / Li, J. / Yong, E.-L. / Xu, H.E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Identification and mechanism of ABA receptor antagonism.
Authors: Melcher, K. / Xu, Y. / Ng, L.M. / Zhou, X.E. / Soon, F.F. / Chinnusamy, V. / Suino-Powell, K.M. / Kovach, A. / Tham, F.S. / Cutler, S.R. / Li, J. / Yong, E.L. / Zhu, J.K. / Xu, H.E.
History
DepositionJun 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_ref_seq_dif / struct_site
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_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.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_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_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_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)56,3316
Polymers55,8812
Non-polymers4504
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-30 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.129, 97.587, 134.505
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 20096.600 Da / Num. of mol.: 1 / Mutation: A93F
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 / References: UniProt: O80992
#2: Protein Protein phosphatase 2C 77 / AtPP2C77 / Protein phosphatase 2C ABI2 / PP2C ABI2 / Protein ABSCISIC ACID-INSENSITIVE 2


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
References: UniProt: O04719, protein-serine/threonine phosphatase
#3: Chemical ChemComp-PYV / 4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide / Pyrabactin


Mass: 377.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13BrN2O2S
#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.: 171 / 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: 3.65 Å3/Da / Density % sol: 66.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 10% PEG 8000, 10% sucrose, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 44745 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 32.4

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3NMT

3nmt


Resolution: 2.1→29.6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.592 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22281 3471 7.2 %RANDOM
Rwork0.19341 ---
all0.19553 ---
obs0.19553 41807 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.284 Å2
Baniso -1Baniso -2Baniso -3
1--2.61 Å20 Å20 Å2
2--5.53 Å20 Å2
3----2.92 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3574 0 25 171 3770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223670
X-RAY DIFFRACTIONr_bond_other_d0.0010.022514
X-RAY DIFFRACTIONr_angle_refined_deg1.951.9624971
X-RAY DIFFRACTIONr_angle_other_deg1.0736113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7545452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07123.576165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00715631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8421529
X-RAY DIFFRACTIONr_chiral_restr0.1330.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214055
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02745
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_it2.081.52269
X-RAY DIFFRACTIONr_mcbond_other0.7531.5917
X-RAY DIFFRACTIONr_mcangle_it3.49723685
X-RAY DIFFRACTIONr_scbond_it4.73631401
X-RAY DIFFRACTIONr_scangle_it7.1114.51286
X-RAY DIFFRACTIONr_rigid_bond_restr2.55936184
X-RAY DIFFRACTIONr_sphericity_free19.2155174
X-RAY DIFFRACTIONr_sphericity_bonded11.75856110
LS refinement shellResolution: 2.1→2.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 256 -
Rwork0.237 3199 -
obs--98.57 %

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