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- PDB-5vsr: ABA-mimicking ligand AMF4 in complex with ABA receptor PYL2 and P... -

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Basic information

Entry
Database: PDB / ID: 5vsr
TitleABA-mimicking ligand AMF4 in complex with ABA receptor PYL2 and PP2C HAB1
Components
  • Abscisic acid receptor PYL2
  • Protein phosphatase 2C 16
KeywordsTRANSFERASE / AMF / ABA / receptor / agonist / drought resistance
Function / homology
Function and homology information


protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / signaling receptor activity / protein homodimerization activity / identical protein binding ...protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / signaling receptor activity / 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-AF0 / Abscisic acid receptor PYL2 / Protein phosphatase 2C 16
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.618 Å
AuthorsCao, M.-J. / Zhang, Y.-L. / Liu, X. / Huang, H. / Zhou, X.E. / Wang, W.-L. / Zeng, A. / Zhao, C.-Z. / Si, T. / Du, J.-M. ...Cao, M.-J. / Zhang, Y.-L. / Liu, X. / Huang, H. / Zhou, X.E. / Wang, W.-L. / Zeng, A. / Zhao, C.-Z. / Si, T. / Du, J.-M. / Wu, W.-W. / Wang, F.-X. / Xu, H.X. / Zhu, J.-K.
CitationJournal: Nat Commun / Year: 2017
Title: Combining chemical and genetic approaches to increase drought resistance in plants.
Authors: Cao, M.J. / Zhang, Y.L. / Liu, X. / Huang, H. / Zhou, X.E. / Wang, W.L. / Zeng, A. / Zhao, C.Z. / Si, T. / Du, J. / Wu, W.W. / Wang, F.X. / Xu, H.E. / Zhu, J.K.
History
DepositionMay 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Abscisic acid receptor PYL2
B: Protein phosphatase 2C 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2496
Polymers57,7322
Non-polymers5174
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-41 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.210, 64.380, 144.830
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: 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 / Production host: Escherichia coli (E. coli) / References: UniProt: O80992
#2: Protein Protein phosphatase 2C 16 / AtPP2C16 / AtP2C-HA / Protein HYPERSENSITIVE TO ABA 1 / Protein phosphatase 2C HAB1 / PP2C HAB1


Mass: 37826.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HAB1, P2C-HA, At1g72770, F28P22.4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase
#3: Chemical ChemComp-AF0 / N-(2-oxo-1-propyl-1,2,3,4-tetrahydroquinolin-6-yl)-1-(2,3,5,6-tetrafluoro-4-methylphenyl)methanesulfonamide / AMF4


Mass: 444.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20F4N2O3S
#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.: 18 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2M Magnesium formate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 1.2544 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2544 Å / Relative weight: 1
ReflectionResolution: 2.62→72.4 Å / Num. obs: 17605 / % possible obs: 99.3 % / Redundancy: 5.7 % / CC1/2: 0.993 / Net I/σ(I): 10.3
Reflection shellResolution: 2.62→2.76 Å / CC1/2: 0.559

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.618→38.624 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 1186 6.82 %
Rwork0.2389 --
obs0.2415 17388 98.87 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.618→38.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3767 0 33 18 3818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043872
X-RAY DIFFRACTIONf_angle_d0.9925241
X-RAY DIFFRACTIONf_dihedral_angle_d15.2811438
X-RAY DIFFRACTIONf_chiral_restr0.04586
X-RAY DIFFRACTIONf_plane_restr0.004674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6181-2.71160.42681030.3981503X-RAY DIFFRACTION95
2.7116-2.82020.44951050.37021592X-RAY DIFFRACTION98
2.8202-2.94850.3997920.34811610X-RAY DIFFRACTION99
2.9485-3.10390.35031180.30891603X-RAY DIFFRACTION100
3.1039-3.29820.34191230.25541613X-RAY DIFFRACTION100
3.2982-3.55270.28211390.24091629X-RAY DIFFRACTION100
3.5527-3.90990.25071060.22391618X-RAY DIFFRACTION100
3.9099-4.4750.24851320.19231632X-RAY DIFFRACTION100
4.475-5.63520.2211480.1891638X-RAY DIFFRACTION99
5.6352-38.62790.23461200.21051764X-RAY DIFFRACTION99

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