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- PDB-4wvo: An engineered PYR1 mandipropamid receptor in complex with mandipr... -

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Basic information

Entry
Database: PDB / ID: 4wvo
TitleAn engineered PYR1 mandipropamid receptor in complex with mandipropamid and HAB1
Components
  • Abscisic acid receptor PYR1
  • Protein phosphatase 2C 16
KeywordsHYDROLASE/HYDROLASE INTHIBITOR / PYR/PYL/RCAR / PYR1 / Hab1 / mandipropamid / PP2C inhibitor / HYDROLASE-HYDROLASE INTHIBITOR complex
Function / homology
Function and homology information


positive regulation of response to water deprivation / plant-type vacuole membrane / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / ubiquitin-like protein ligase binding / signaling receptor activity ...positive regulation of response to water deprivation / plant-type vacuole membrane / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / ubiquitin-like protein ligase binding / signaling receptor activity / protein homodimerization activity / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Polyketide cyclase / dehydrase and lipid transport / 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 ...Polyketide cyclase / dehydrase and lipid transport / 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-3UZ / Abscisic acid receptor PYR1 / Protein phosphatase 2C 16
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.251 Å
AuthorsPeterson, F.C. / Volkman, B.F. / Cutler, S.R.
CitationJournal: Nature / Year: 2015
Title: Agrochemical control of plant water use using engineered abscisic acid receptors.
Authors: Park, S.Y. / Peterson, F.C. / Mosquna, A. / Yao, J. / Volkman, B.F. / Cutler, S.R.
History
DepositionNov 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Nov 2, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / citation ...chem_comp / citation / database_2 / entity_src_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.journal_id_CSD ..._chem_comp.pdbx_synonyms / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _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.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_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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.4Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Abscisic acid receptor PYR1
B: Protein phosphatase 2C 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7276
Polymers57,2422
Non-polymers4854
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-42 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.459, 66.999, 172.019
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 PYR1 / ABI1-binding protein 6 / Protein PYRABACTIN RESISTANCE 1 / Regulatory components of ABA receptor 11


Mass: 20659.332 Da / Num. of mol.: 1 / Mutation: K59R V81I F108A F159L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYR1, ABIP6, RCAR11, At4g17870, T6K21.50 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O49686
#2: Protein Protein phosphatase 2C 16 / AtPP2C16 / AtP2C-HA / Protein HYPERSENSITIVE TO ABA 1 / Protein phosphatase 2C HAB1 / PP2C HAB1


Mass: 36582.891 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 / Plasmid: pET11M / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase
#3: Chemical ChemComp-3UZ / (2S)-2-(4-chlorophenyl)-N-{2-[3-methoxy-4-(prop-2-yn-1-yloxy)phenyl]ethyl}-2-(prop-2-yn-1-yloxy)ethanamide / Mandipropamid


Mass: 411.878 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22ClNO4
#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.: 192 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22.5% PEG 2000 mono methyl ether 150 mM Sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 25330 / % possible obs: 98.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 23.6
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 6 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.1 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3QN1

3qn1


Resolution: 2.251→36.191 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 1885 7.91 %Random selection
Rwork0.1825 ---
obs0.1862 23834 92.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.251→36.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3684 0 32 192 3908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123792
X-RAY DIFFRACTIONf_angle_d1.1495119
X-RAY DIFFRACTIONf_dihedral_angle_d14.181420
X-RAY DIFFRACTIONf_chiral_restr0.071572
X-RAY DIFFRACTIONf_plane_restr0.006660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2512-2.3120.32681190.25051462X-RAY DIFFRACTION81
2.312-2.38010.30881290.24011469X-RAY DIFFRACTION83
2.3801-2.45690.33571340.23031555X-RAY DIFFRACTION88
2.4569-2.54460.26641370.22681557X-RAY DIFFRACTION87
2.5446-2.64650.3451370.22591636X-RAY DIFFRACTION91
2.6465-2.76690.28061450.21531656X-RAY DIFFRACTION92
2.7669-2.91270.29181460.22091686X-RAY DIFFRACTION93
2.9127-3.09510.27621480.20881709X-RAY DIFFRACTION95
3.0951-3.33390.27141510.19361768X-RAY DIFFRACTION97
3.3339-3.66920.23061560.17151808X-RAY DIFFRACTION99
3.6692-4.19940.19751560.15081833X-RAY DIFFRACTION99
4.1994-5.28820.17391590.14271846X-RAY DIFFRACTION99
5.2882-36.19550.17561680.17761964X-RAY DIFFRACTION99
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)
12.387-0.21260.69271.91120.79215.9639-0.1284-0.1884-0.00360.22750.04790.09550.3033-0.05530.07380.29910.01890.01210.2948-0.05680.32724.539122.0381215.1733
20.9659-0.0197-0.08961.2915-0.28841.21990.0370.0374-0.0491-0.0866-0.0189-0.0710.20510.0507-0.02270.22850.0048-0.02130.2814-0.02040.28681.73773.681181.5599
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A)A3 - 180
2X-RAY DIFFRACTION2(chain B)B186 - 505

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