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- PDB-5gwp: Crystal structure of RCAR3:PP2C wild-type with (+)-ABA -

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Basic information

Entry
Database: PDB / ID: 5gwp
TitleCrystal structure of RCAR3:PP2C wild-type with (+)-ABA
Components
  • ABA receptor RCAR3
  • Probable protein phosphatase 2C 50
KeywordsHYDROLASE/RECEPTOR / abscisic acid / ABA receptor / PP2C / HYDROLASE-RECEPTOR 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: 2.577 Å
AuthorsHan, S. / Lee, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Rural Development AgencyPJ009106 Korea, Republic Of
CitationJournal: Mol Plant / Year: 2017
Title: Modulation of ABA Signaling by Altering VxG Phi L Motif of PP2Cs in Oryza sativa.
Authors: Han, S. / Min, M.K. / Lee, S.Y. / Lim, C.W. / Bhatnagar, N. / Lee, Y. / Shin, D. / Chung, K.Y. / Lee, S.C. / Kim, B.G. / Lee, S.
History
DepositionSep 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_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 1.3Nov 6, 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
B: Probable protein phosphatase 2C 50
C: ABA receptor RCAR3
D: ABA receptor RCAR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,81112
Polymers111,1374
Non-polymers6748
Water1,40578
1
A: Probable protein phosphatase 2C 50
C: ABA receptor RCAR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9066
Polymers55,5682
Non-polymers3374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-36 kcal/mol
Surface area21170 Å2
MethodPISA
2
B: Probable protein phosphatase 2C 50
D: ABA receptor RCAR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9066
Polymers55,5682
Non-polymers3374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-37 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.981, 133.684, 191.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 35507.512 Da / Num. of mol.: 2 / Fragment: UNP residues 59-385 / Mutation: E139A/E140A/K142A
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 / Fragment: UNP residues 30-204
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.: 6 / 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.: 78 / 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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 8000, MES pH 6.0, calcium acetate

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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: Oct 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.577→46.1435 Å / Num. obs: 30728 / % possible obs: 96 % / Redundancy: 11 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1142 / Rsym value: 0.12 / Net I/σ(I): 22.02
Reflection shellResolution: 2.577→2.67 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RT0

3rt0


Resolution: 2.577→46.136 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 0 / Phase error: 27.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2467 1928 6.53 %
Rwork0.206 --
obs0.2087 29514 95.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.577→46.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7134 0 44 78 7256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027294
X-RAY DIFFRACTIONf_angle_d0.5199872
X-RAY DIFFRACTIONf_dihedral_angle_d14.2954460
X-RAY DIFFRACTIONf_chiral_restr0.0441127
X-RAY DIFFRACTIONf_plane_restr0.0041283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5775-2.64190.32151320.25791812X-RAY DIFFRACTION89
2.6419-2.71330.30941220.27051812X-RAY DIFFRACTION90
2.7133-2.79320.34551370.26351856X-RAY DIFFRACTION92
2.7932-2.88330.31651230.26771890X-RAY DIFFRACTION93
2.8833-2.98630.27441470.24951916X-RAY DIFFRACTION94
2.9863-3.10590.26841230.23181942X-RAY DIFFRACTION95
3.1059-3.24720.29171400.21441971X-RAY DIFFRACTION97
3.2472-3.41840.27141330.22121992X-RAY DIFFRACTION97
3.4184-3.63240.24861480.20972001X-RAY DIFFRACTION98
3.6324-3.91280.23081380.19122014X-RAY DIFFRACTION98
3.9128-4.30630.19321420.17342044X-RAY DIFFRACTION99
4.3063-4.92880.20461480.15792066X-RAY DIFFRACTION100
4.9288-6.20740.23251430.19492098X-RAY DIFFRACTION100
6.2074-46.14350.23711520.2062172X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -38.7842 Å / Origin y: -13.2151 Å / Origin z: -23.3851 Å
111213212223313233
T0.3113 Å2-0.0445 Å2-0.0711 Å2-0.3265 Å20.0285 Å2--0.3351 Å2
L0.6165 °2-0.2387 °2-0.0679 °2-0.7975 °20.0396 °2--0.3626 °2
S-0.0105 Å °-0.0828 Å °-0.0991 Å °-0.0584 Å °0.0072 Å °0.1535 Å °-0.0062 Å °-0.0089 Å °0.0029 Å °
Refinement TLS groupSelection details: all

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