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- PDB-5zcl: Crystal structure of OsPP2C50 I267L:OsPYL/RCAR3 with (+)-ABA -

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Basic information

Entry
Database: PDB / ID: 5zcl
TitleCrystal structure of OsPP2C50 I267L:OsPYL/RCAR3 with (+)-ABA
Components
  • ABA receptor RCAR3
  • Probable protein phosphatase 2C 50
KeywordsPLANT PROTEIN / abscisic acid / ABA / receptor / phosphatase / stress / complex
Function / homology
Function and homology information


regulation of intracellular signal transduction / seed germination / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / protein serine/threonine phosphatase activity / protein phosphatase inhibitor activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity ...regulation of intracellular signal transduction / seed germination / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / protein serine/threonine phosphatase activity / protein phosphatase inhibitor activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin 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 / Abscisic acid receptor PYL3 / Protein phosphatase 2C 50
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
Oryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.661 Å
AuthorsLee, S. / Han, S.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
the Rural Development AgencyPJ013676 Korea, Republic Of
the National Research Foundation of KoreaNRF-2017R1D1A1B03032185 Korea, Republic Of
the National Research Foundation of KoreaSRC-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 19, 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 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable protein phosphatase 2C 50
C: ABA receptor RCAR3
B: Probable protein phosphatase 2C 50
D: ABA receptor RCAR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,90510
Polymers111,2794
Non-polymers6266
Water1,29772
1
A: Probable protein phosphatase 2C 50
C: ABA receptor RCAR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9525
Polymers55,6392
Non-polymers3133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-30 kcal/mol
Surface area21290 Å2
MethodPISA
2
B: Probable protein phosphatase 2C 50
D: ABA receptor RCAR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9525
Polymers55,6392
Non-polymers3133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-30 kcal/mol
Surface area21440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.096, 130.262, 80.252
Angle α, β, γ (deg.)90.00, 115.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable protein phosphatase 2C 50 / OsPP2C50


Mass: 35578.594 Da / Num. of mol.: 2 / Mutation: E139A/E140A/K142A/I267L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Os05g0537400, LOC_Os05g46040, OJ1741_B01.18, OSJNBa0052K01.2
Production host: Escherichia coli (E. coli)
References: UniProt: Q6L5H6, protein-serine/threonine phosphatase
#2: Protein ABA receptor RCAR3


Mass: 20060.865 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Production host: Escherichia coli (E. coli) / References: UniProt: K4N2F7, UniProt: Q6EN42*PLUS
#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


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


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.17 Å3/Da / Density % sol: 61.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 12% (w/v) PEG 8000, 0.3M Mg(OAc)2, 0.1M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 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: 2.661→38.149 Å / Num. obs: 39539 / % possible obs: 99.27 % / Redundancy: 4.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.1204 / Rpim(I) all: 0.0662 / Net I/σ(I): 9.22
Reflection shellResolution: 2.661→2.757 Å / Rmerge(I) obs: 0.708 / Num. unique obs: 3799 / CC1/2: 0.648 / Rpim(I) all: 0.4107

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GWP

5gwp


Resolution: 2.661→38.149 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.32
RfactorNum. reflection% reflection
Rfree0.2397 2003 5.07 %
Rwork0.1952 --
obs0.1975 39494 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.661→38.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7276 0 42 72 7390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057442
X-RAY DIFFRACTIONf_angle_d0.70610078
X-RAY DIFFRACTIONf_dihedral_angle_d12.9294533
X-RAY DIFFRACTIONf_chiral_restr0.0491142
X-RAY DIFFRACTIONf_plane_restr0.0051319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6615-2.7280.37131390.30562513X-RAY DIFFRACTION94
2.728-2.80170.31091420.27232657X-RAY DIFFRACTION99
2.8017-2.88410.34051400.24642705X-RAY DIFFRACTION100
2.8841-2.97720.24771410.23622661X-RAY DIFFRACTION100
2.9772-3.08360.27891450.2242695X-RAY DIFFRACTION100
3.0836-3.2070.27471450.22412682X-RAY DIFFRACTION100
3.207-3.35280.30831450.22222674X-RAY DIFFRACTION100
3.3528-3.52950.27381390.21242676X-RAY DIFFRACTION100
3.5295-3.75040.25841470.19662724X-RAY DIFFRACTION100
3.7504-4.03970.23551420.18762677X-RAY DIFFRACTION100
4.0397-4.44570.21151400.16342698X-RAY DIFFRACTION100
4.4457-5.08770.18761450.1572712X-RAY DIFFRACTION100
5.0877-6.40510.20691470.1792698X-RAY DIFFRACTION100
6.4051-38.15330.18021460.16772719X-RAY DIFFRACTION99

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