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- PDB-5zcg: Crystal structure of OsPP2C50 S265L/I267V:OsPYL/RCAR3 with (+)-ABA -

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Basic information

Entry
Database: PDB / ID: 5zcg
TitleCrystal structure of OsPP2C50 S265L/I267V:OsPYL/RCAR3 with (+)-ABA
Components
  • ABA receptor RCAR3
  • Probable protein phosphatase 2C 50Probability
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 / 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: 2.1 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 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 1.2Nov 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

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


Theoretical massNumber of molelcules
Total (without water)111,92910
Polymers111,3034
Non-polymers6266
Water9,350519
1
A: Probable protein phosphatase 2C 50
C: ABA receptor RCAR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9645
Polymers55,6522
Non-polymers3133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-27 kcal/mol
Surface area20650 Å2
MethodPISA
2
B: Probable protein phosphatase 2C 50
D: ABA receptor RCAR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9645
Polymers55,6522
Non-polymers3133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-29 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.738, 76.351, 77.942
Angle α, β, γ (deg.)62.96, 72.04, 66.93
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 35590.645 Da / Num. of mol.: 2 / Mutation: E139A/E140A/K142A/S265L/I267V
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 / 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.: 519 / 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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 7.5% PEG 3350, 80mM ammonium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.97→32.95 Å / Num. obs: 89408 / % possible obs: 95.82 % / Redundancy: 3.2 % / Biso Wilson estimate: 32.32 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.0675 / Rpim(I) all: 0.04617 / Net I/σ(I): 16.61
Reflection shellResolution: 1.97→2.041 Å / Rmerge(I) obs: 0.3323 / Num. unique obs: 7413 / CC1/2: 0.912 / Rpim(I) all: 0.2208

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GWP

5gwp


Resolution: 2.1→32.946 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 26.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2373 1616 2.25 %
Rwork0.202 --
obs0.2028 71944 93.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→32.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7315 0 42 519 7876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047497
X-RAY DIFFRACTIONf_angle_d0.93110150
X-RAY DIFFRACTIONf_dihedral_angle_d6.5974572
X-RAY DIFFRACTIONf_chiral_restr0.1021154
X-RAY DIFFRACTIONf_plane_restr0.0051326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16180.35921260.26255460X-RAY DIFFRACTION87
2.1618-2.23150.30371310.24565618X-RAY DIFFRACTION89
2.2315-2.31130.29031310.23345729X-RAY DIFFRACTION91
2.3113-2.40380.26171300.22635749X-RAY DIFFRACTION92
2.4038-2.51320.25461380.21515886X-RAY DIFFRACTION93
2.5132-2.64560.24321360.2115901X-RAY DIFFRACTION95
2.6456-2.81130.21861370.20586013X-RAY DIFFRACTION96
2.8113-3.02820.24521390.20386019X-RAY DIFFRACTION96
3.0282-3.33270.2211370.20046041X-RAY DIFFRACTION96
3.3327-3.81430.25571390.18995999X-RAY DIFFRACTION95
3.8143-4.80330.19911320.17715837X-RAY DIFFRACTION93
4.8033-32.95020.22131400.20096076X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 39.895 Å / Origin y: 15.6373 Å / Origin z: -7.8482 Å
111213212223313233
T0.2118 Å20.0011 Å2-0.0015 Å2-0.1964 Å2-0.0145 Å2--0.1856 Å2
L0.4738 °2-0.0224 °20.1503 °2-0.427 °20.1549 °2--0.5045 °2
S-0.009 Å °-0.022 Å °0.0089 Å °-0.0488 Å °0.003 Å °-0.0182 Å °-0.0139 Å °-0.0148 Å °0.0064 Å °
Refinement TLS groupSelection details: all

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