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- PDB-4lgb: ABA-mimicking ligand N-(1-METHYL-2-OXO-1,2,3,4-TETRAHYDROQUINOLIN... -

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Basic information

Entry
Database: PDB / ID: 4lgb
TitleABA-mimicking ligand N-(1-METHYL-2-OXO-1,2,3,4-TETRAHYDROQUINOLIN-6-YL)-1-(4-METHYLPHENYL)METHANESULFONAMIDE in complex with ABA receptor PYL2 and PP2C HAB1
Components
  • Abscisic acid receptor PYL2
  • Protein phosphatase 2C 16
KeywordsHydrolase/receptor / abscisic acid mimicking compounds / PYR/PYL/RCAR / PP2C / Hydrolase-receptor complex
Function / homology
Function and homology information


protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / myosin phosphatase activity / protein serine/threonine 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 / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / signaling receptor activity / protein homodimerization activity / identical protein binding / metal ion 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-1W7 / Abscisic acid receptor PYL2 / Protein phosphatase 2C 16
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsZhou, X.E. / Gao, M. / Liu, X. / Zhang, Y. / Xue, X. / Melcher, K. / Gao, P. / Wang, F. / Zeng, L. / Zhao, Y. ...Zhou, X.E. / Gao, M. / Liu, X. / Zhang, Y. / Xue, X. / Melcher, K. / Gao, P. / Wang, F. / Zeng, L. / Zhao, Y. / Zhao, Y. / Deng, P. / Zhong, D. / Zhu, J.-K. / Xu, Y. / Xu, H.E.
CitationJournal: Cell Res. / Year: 2013
Title: An ABA-mimicking ligand that reduces water loss and promotes drought resistance in plants.
Authors: Cao, M. / Liu, X. / Zhang, Y. / Xue, X. / Zhou, X.E. / Melcher, K. / Gao, P. / Wang, F. / Zeng, L. / Zhao, Y. / Zhao, Y. / Deng, P. / Zhong, D. / Zhu, J.K. / Xu, H.E. / Xu, Y.
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 20, 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_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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3897
Polymers57,7322
Non-polymers6575
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-65 kcal/mol
Surface area21790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.957, 66.173, 143.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 19905.414 Da / Num. of mol.: 1 / Fragment: unp residues 14-188
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) / Strain (production host): BL21(DE3) / 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 / Fragment: unp residues 172-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g72770, F28P22.4, HAB1, P2C-HA / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase

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Non-polymers , 4 types, 38 molecules

#3: Chemical ChemComp-1W7 / N-(1-methyl-2-oxo-1,2,3,4-tetrahydroquinolin-6-yl)-1-(4-methylphenyl)methanesulfonamide


Mass: 344.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N2O3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.52 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG3350, ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→30 Å / Num. all: 10654 / Num. obs: 8417 / % possible obs: 79 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 4.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.15-3.263.60.558158.2
3.26-3.394.50.499184.4
3.39-3.554.40.444183.3
3.55-3.734.50.362182.5
3.73-3.974.40.277182
3.97-4.274.60.198182
4.27-4.74.50.146181.4
4.7-5.384.40.119180.8
5.38-6.764.50.118179
6.76-304.50.051176

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
CNSrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASESphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3KB3

3kb3


Resolution: 3.15→30 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.864 / Occupancy max: 1 / Occupancy min: 1 / SU B: 32.772 / SU ML: 0.504 / Cross valid method: THROUGHOUT / ESU R Free: 0.73 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29387 843 10.1 %RANDOM
Rwork0.26982 ---
obs0.27219 7543 79.45 %-
all-8417 --
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: 57.048 Å2
Baniso -1Baniso -2Baniso -3
1--7.71 Å20 Å20 Å2
2--10.77 Å20 Å2
3----3.05 Å2
Refinement stepCycle: LAST / Resolution: 3.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3673 0 40 33 3746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223780
X-RAY DIFFRACTIONr_bond_other_d0.0030.022591
X-RAY DIFFRACTIONr_angle_refined_deg1.0131.9685112
X-RAY DIFFRACTIONr_angle_other_deg0.82836297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1545462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24523.529170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36215660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.681531
X-RAY DIFFRACTIONr_chiral_restr0.0550.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214151
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02763
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_it1.0681.52323
X-RAY DIFFRACTIONr_mcbond_other0.071.5946
X-RAY DIFFRACTIONr_mcangle_it1.94823759
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.97431457
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8224.51353
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.15→3.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 33 -
Rwork0.369 389 -
obs--56.04 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.paramCNS_TOPPAR:carbohydrate.top
X-RAY DIFFRACTION6A20_par2.txtA20_top2.txt
X-RAY DIFFRACTION7so4_xplor_par.txtso4_xplor_top.txt

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