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- PDB-4n0g: Crystal Structure of PYL13-PP2CA complex -

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Basic information

Entry
Database: PDB / ID: 4n0g
TitleCrystal Structure of PYL13-PP2CA complex
Components
  • Abscisic acid receptor PYL13
  • Protein phosphatase 2C 37
KeywordsHYDROLASE/RECEPTOR / ABA receptor/phosphatase / HYDROLASE-RECEPTOR complex
Function / homology
Function and homology information


negative regulation of abscisic acid-activated signaling pathway / negative regulation of anion channel activity / regulation of stomatal movement / response to abscisic acid / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein serine/threonine phosphatase activity / myosin phosphatase activity ...negative regulation of abscisic acid-activated signaling pathway / negative regulation of anion channel activity / regulation of stomatal movement / response to abscisic acid / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / phosphoprotein phosphatase activity / response to cold / kinase binding / signaling receptor activity / defense response to virus / protein kinase binding / protein homodimerization activity / nucleus / metal ion binding / plasma membrane / 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
Protein phosphatase 2C 37 / Abscisic acid receptor PYL13
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.382 Å
AuthorsLi, W. / Wang, L. / Sheng, X. / Yan, C. / Zhou, R. / Hang, J. / Yin, P. / Yan, N.
CitationJournal: Cell Res. / Year: 2013
Title: Molecular basis for the selective and ABA-independent inhibition of PP2CA by PYL13
Authors: Li, W. / Wang, L. / Sheng, X. / Yan, C. / Zhou, R. / Hang, J. / Yin, P. / Yan, N.
History
DepositionOct 1, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein phosphatase 2C 37
B: Protein phosphatase 2C 37
C: Abscisic acid receptor PYL13
D: Abscisic acid receptor PYL13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,39816
Polymers108,0244
Non-polymers37412
Water5,531307
1
A: Protein phosphatase 2C 37
C: Abscisic acid receptor PYL13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1998
Polymers54,0122
Non-polymers1876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-46 kcal/mol
Surface area18020 Å2
MethodPISA
2
B: Protein phosphatase 2C 37
D: Abscisic acid receptor PYL13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1998
Polymers54,0122
Non-polymers1876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-46 kcal/mol
Surface area17600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.383, 111.383, 70.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Protein phosphatase 2C 37 / AtPP2C37 / Protein ABA-HYPERSENSITIVE GERMINATION 3 / Protein phosphatase 2C A / PP2CA


Mass: 35859.293 Da / Num. of mol.: 2 / Fragment: UNP residues 72-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PP2CA, AHG3, At3g11410, F24K9.8 / Production host: Escherichia coli (E. coli)
References: UniProt: P49598, protein-serine/threonine phosphatase
#2: Protein Abscisic acid receptor PYL13 / PYR1-like protein 13 / Regulatory components of ABA receptor 7


Mass: 18152.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL13, RCAR7, At4g18620, F28A21.30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SN51
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES pH 6.5, 25% PEG600, 150mM Calcium Chloride, 2.7% 2,5-Hexanediol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→40 Å / Num. all: 39034 / Num. obs: 38995 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.38→2.47 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RTO

3rto


Resolution: 2.382→39.79 Å / SU ML: 0.32 / σ(F): 1.97 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 1952 5.01 %RANDOM
Rwork0.2108 ---
obs0.2125 38972 99.82 %-
all-39050 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.677 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5691 Å20 Å2-0 Å2
2--2.5691 Å20 Å2
3----5.1383 Å2
Refinement stepCycle: LAST / Resolution: 2.382→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6350 0 12 307 6669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096448
X-RAY DIFFRACTIONf_angle_d1.178719
X-RAY DIFFRACTIONf_dihedral_angle_d16.8422406
X-RAY DIFFRACTIONf_chiral_restr0.0781024
X-RAY DIFFRACTIONf_plane_restr0.0081122
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.382-2.44190.34161440.2768260599
2.4419-2.50790.30831280.2772611100
2.5079-2.58170.27681340.25942677100
2.5817-2.6650.33211330.2692646100
2.665-2.76020.26571240.27062643100
2.7602-2.87070.34621520.25312689100
2.8707-3.00130.27061470.24962646100
3.0013-3.15950.2761440.23852642100
3.1595-3.35740.2711330.21462622100
3.3574-3.61640.20361460.20582634100
3.6164-3.98010.25261400.19452715100
3.9801-4.55530.21081430.16632611100
4.5553-5.73640.1851370.17552655100
5.7364-39.79580.21621470.1863262499
Refinement TLS params.Method: refined / Origin x: 28.886 Å / Origin y: -16.696 Å / Origin z: -9.9159 Å
111213212223313233
T0.2149 Å20.0081 Å2-0.0255 Å2-0.2447 Å2-0.0377 Å2--0.2355 Å2
L0.1736 °20.0729 °2-0.1279 °2-0.1536 °2-0.1155 °2--0.1942 °2
S0.0058 Å °-0.0258 Å °0.0202 Å °-0.0013 Å °-0.0178 Å °0.0004 Å °-0.0099 Å °0.0323 Å °0.0051 Å °
Refinement TLS groupSelection details: all

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