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- PDB-5zch: Crystal structure of OsPP2C50 I267W:OsPYL/RCAR3 with (+)-ABA -

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Basic information

Entry
Database: PDB / ID: 5zch
TitleCrystal structure of OsPP2C50 I267W:OsPYL/RCAR3 with (+)-ABA
Components
  • Abscisic acid receptor PYL3
  • Protein phosphatase 2C 50
KeywordsPLANT PROTEIN / abscisic acid / ABA / receptor / phosphatase / stress / complex
Function / homology
Function and homology information


negative regulation of protein serine/threonine phosphatase activity / seed germination / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / response to cold ...negative regulation of protein serine/threonine phosphatase activity / seed germination / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / response to cold / signaling receptor activity / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Sigma factor PP2C-like phosphatases / 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 ...Sigma factor PP2C-like phosphatases / 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 / Abscisic acid receptor PYL3 / Protein phosphatase 2C 50
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.474 Å
AuthorsLee, S. / Han, S.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
Rural Development AdministrationPJ013676 Korea, Republic Of
National Research Foundation (Korea)NRF-2017R1D1A1B03032185 Korea, Republic Of
National Research Foundation (Korea)SRC-2017R1A5A1014560 Korea, Republic Of
CitationJournal: Plant Mol.Biol. / Year: 2019
Title: Comprehensive survey of the VxG Phi L motif of PP2Cs from Oryza sativa reveals the critical role of the fourth position in regulation of ABA responsiveness.
Authors: Han, S. / Lee, J.Y. / Lee, Y. / Kim, T.H. / Lee, S.
History
DepositionFeb 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein phosphatase 2C 50
C: Abscisic acid receptor PYL3
B: Protein phosphatase 2C 50
D: Abscisic acid receptor PYL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,05110
Polymers111,4254
Non-polymers6266
Water2,954164
1
A: Protein phosphatase 2C 50
C: Abscisic acid receptor PYL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0255
Polymers55,7132
Non-polymers3133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-29 kcal/mol
Surface area20270 Å2
MethodPISA
2
B: Protein phosphatase 2C 50
D: Abscisic acid receptor PYL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0255
Polymers55,7132
Non-polymers3133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-29 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.731, 76.028, 78.586
Angle α, β, γ (deg.)62.30, 73.09, 65.01
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein phosphatase 2C 50 / OsPP2C50 / ABI1-like protein 3 / OsABIL3


Mass: 35651.645 Da / Num. of mol.: 2 / Mutation: E139A/E140A/K142A/I267W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: PP2C50, ABIL3, Os05g0537400, LOC_Os05g46040, OJ1741_B01.18, OSJNBa0052K01.2
Production host: Escherichia coli (E. coli)
References: UniProt: Q6L5H6, protein-serine/threonine phosphatase
#2: Protein Abscisic acid receptor PYL3 / PYR1-like protein 10 / OsPYL10 / PYR1-like protein 3 / OsPYL3 / Regulatory components of ABA receptor 3


Mass: 20060.865 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: PYL3, PYL10, RCAR3, Os02g0255500, LOC_Os02g15640, OSJNBa0052K15.19, P0613F08.1
Production host: Escherichia coli (E. coli) / References: UniProt: Q6EN42
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: 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 / Abscisic acid


Mass: 264.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H20O4 / Comment: hormone*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 20% v/v PEG 400, 5% w/v PEG 3000, 10% v/v glycerol, 0.1M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.474→24.788 Å / Num. obs: 45783 / % possible obs: 96.87 % / Redundancy: 3.2 % / Net I/σ(I): 15.16
Reflection shellResolution: 2.474→2.563 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.474→24.788 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.39
RfactorNum. reflection% reflection
Rfree0.2303 1998 4.37 %
Rwork0.206 --
obs0.2072 45737 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.474→24.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7130 0 42 164 7336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037289
X-RAY DIFFRACTIONf_angle_d0.6719867
X-RAY DIFFRACTIONf_dihedral_angle_d7.2644445
X-RAY DIFFRACTIONf_chiral_restr0.0511123
X-RAY DIFFRACTIONf_plane_restr0.0041288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4735-2.53530.3441260.29272757X-RAY DIFFRACTION86
2.5353-2.60380.33941430.28373105X-RAY DIFFRACTION97
2.6038-2.68030.29361450.27333170X-RAY DIFFRACTION98
2.6803-2.76670.29971440.26723164X-RAY DIFFRACTION98
2.7667-2.86550.30281440.25973150X-RAY DIFFRACTION98
2.8655-2.980.31121440.25163160X-RAY DIFFRACTION98
2.98-3.11540.30251430.24123150X-RAY DIFFRACTION98
3.1154-3.27930.25321450.23333145X-RAY DIFFRACTION98
3.2793-3.48420.25681450.22463165X-RAY DIFFRACTION98
3.4842-3.75240.20181440.20463163X-RAY DIFFRACTION98
3.7524-4.12850.21231420.18383135X-RAY DIFFRACTION98
4.1285-4.72230.1871450.15983159X-RAY DIFFRACTION97
4.7223-5.93610.17581440.17613164X-RAY DIFFRACTION98
5.9361-24.78960.19341440.1753152X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 16.3507 Å / Origin y: -28.9149 Å / Origin z: -15.0559 Å
111213212223313233
T0.2058 Å2-0.0035 Å20.0229 Å2-0.1897 Å2-0.0063 Å2--0.2092 Å2
L0.4484 °2-0.0619 °2-0.0469 °2-0.5269 °20.0052 °2--0.117 °2
S0.0376 Å °-0.0287 Å °0.0013 Å °-0.0894 Å °0.0283 Å °-0.106 Å °-0.0218 Å °-0.0275 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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