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- PDB-5gwo: Crystal structure of RCAR3:PP2C S265F/I267M with (+)-ABA -

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Basic information

Entry
Database: PDB / ID: 5gwo
TitleCrystal structure of RCAR3:PP2C S265F/I267M with (+)-ABA
Components
  • ABA receptor RCAR3
  • Probable protein phosphatase 2C 50Probability
KeywordsHYDROLASE/RECEPTOR / abscisic acid / ABA receptor / PP2C / HYDROLASE-RECEPTOR 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: 2.816 Å
AuthorsHan, S. / Lee, S.
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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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)111,94311
Polymers111,2934
Non-polymers6507
Water66737
1
A: Probable protein phosphatase 2C 50
C: ABA receptor RCAR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9846
Polymers55,6472
Non-polymers3374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-40 kcal/mol
Surface area21410 Å2
MethodPISA
2
B: Probable protein phosphatase 2C 50
D: ABA receptor RCAR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9595
Polymers55,6472
Non-polymers3133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-32 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.472, 79.253, 80.288
Angle α, β, γ (deg.)81.63, 87.08, 73.98
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 35585.645 Da / Num. of mol.: 2 / Fragment: UNP residues 59-385 / Mutation: E139A/E140A/K142A/S265F/I267M
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.: 5 / 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.: 37 / 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: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, MES pH 6.0, magnesium acetate, glycerol

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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: Mar 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.816→37.729 Å / Num. obs: 25506 / % possible obs: 97 % / Redundancy: 3.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.1066 / Rsym value: 0.1274 / Net I/σ(I): 13.54
Reflection shellResolution: 2.816→2.917 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: 2.816→37.729 Å / SU ML: 0.4 / Cross valid method: NONE / σ(F): 1.98 / Phase error: 27.74
RfactorNum. reflection% reflection
Rfree0.2427 2010 7.88 %
Rwork0.1849 --
obs0.1895 25497 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.816→37.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7367 0 43 37 7447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057537
X-RAY DIFFRACTIONf_angle_d0.93710203
X-RAY DIFFRACTIONf_dihedral_angle_d11.2134599
X-RAY DIFFRACTIONf_chiral_restr0.0951154
X-RAY DIFFRACTIONf_plane_restr0.0051332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.816-2.88630.34651420.27311615X-RAY DIFFRACTION92
2.8863-2.96430.35641490.25591698X-RAY DIFFRACTION99
2.9643-3.05150.30631410.25191705X-RAY DIFFRACTION98
3.0515-3.150.32261560.22471695X-RAY DIFFRACTION99
3.15-3.26250.27681390.21841706X-RAY DIFFRACTION98
3.2625-3.3930.2861420.21381697X-RAY DIFFRACTION98
3.393-3.54730.25651490.20621731X-RAY DIFFRACTION98
3.5473-3.73420.25791420.18161683X-RAY DIFFRACTION98
3.7342-3.96790.23141460.18021710X-RAY DIFFRACTION97
3.9679-4.27390.21891440.16481693X-RAY DIFFRACTION97
4.2739-4.70330.21141460.15381662X-RAY DIFFRACTION96
4.7033-5.38220.20541420.15941649X-RAY DIFFRACTION96
5.3822-6.77460.20941410.18661650X-RAY DIFFRACTION95
6.7746-37.7290.21851310.15831593X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: -37.4819 Å / Origin y: 26.4132 Å / Origin z: -5.9916 Å
111213212223313233
T0.2795 Å2-0.0044 Å20.0225 Å2-0.3224 Å2-0.0188 Å2--0.3403 Å2
L0.4183 °20.0925 °2-0.053 °2-0.9772 °2-0.0684 °2--0.2808 °2
S-0.021 Å °-0.0213 Å °-0.0293 Å °0.0307 Å °-0.0054 Å °-0.1024 Å °0.0068 Å °0.0092 Å °0.0207 Å °
Refinement TLS groupSelection details: all

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