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- PDB-3nmn: Crystal structure of pyrabactin-bound abscisic acid receptor PYL1... -

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Basic information

Entry
Database: PDB / ID: 3nmn
TitleCrystal structure of pyrabactin-bound abscisic acid receptor PYL1 in complex with type 2C protein phosphatase ABI1
Components
  • Abscisic acid receptor PYL1
  • Protein phosphatase 2C 56
KeywordsPROTEIN BINDING / PYL1 / Pyrabactin / Plant hormone receptor / abscisic acid signaling
Function / homology
Function and homology information


regulation of abscisic acid-activated signaling pathway / negative regulation of abscisic acid-activated signaling pathway / protein phosphatase inhibitor complex / regulation of stomatal movement / response to abscisic acid / abscisic acid binding / abscisic acid-activated signaling pathway / plastid / protein serine/threonine phosphatase activity / protein phosphatase inhibitor activity ...regulation of abscisic acid-activated signaling pathway / negative regulation of abscisic acid-activated signaling pathway / protein phosphatase inhibitor complex / regulation of stomatal movement / response to abscisic acid / abscisic acid binding / abscisic acid-activated signaling pathway / plastid / 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 / phosphatase activity / phosphoprotein phosphatase activity / protein dephosphorylation / response to cold / defense response / kinase binding / signaling receptor activity / response to heat / protein kinase binding / protein homodimerization activity / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
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, 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-PYV / Protein phosphatase 2C 56 / Abscisic acid receptor PYL1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsZhou, X.E. / Melcher, K. / Ng, L.-M. / Soon, F.-F. / Xu, Y. / Suino-Powell, K.M. / Kovach, A. / Li, J. / Yong, E.-L. / Xu, H.E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Identification and mechanism of ABA receptor antagonism.
Authors: Melcher, K. / Xu, Y. / Ng, L.M. / Zhou, X.E. / Soon, F.F. / Chinnusamy, V. / Suino-Powell, K.M. / Kovach, A. / Tham, F.S. / Cutler, S.R. / Li, J. / Yong, E.L. / Zhu, J.K. / Xu, H.E.
History
DepositionJun 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif / 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_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Abscisic acid receptor PYL1
B: Protein phosphatase 2C 56
C: Abscisic acid receptor PYL1
D: Protein phosphatase 2C 56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,25810
Polymers111,4064
Non-polymers8526
Water3,243180
1
A: Abscisic acid receptor PYL1
B: Protein phosphatase 2C 56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1295
Polymers55,7032
Non-polymers4263
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-21 kcal/mol
Surface area19200 Å2
MethodPISA
2
C: Abscisic acid receptor PYL1
D: Protein phosphatase 2C 56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1295
Polymers55,7032
Non-polymers4263
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-22 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.978, 66.710, 72.598
Angle α, β, γ (deg.)115.78, 95.43, 105.60
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Abscisic acid receptor PYL1 / PYR1-like protein 1 / ABI1-binding protein 6 / Regulatory components of ABA receptor 9


Mass: 20534.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL1, RCAR12, At5g46790, MZA15.21 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8VZS8
#2: Protein Protein phosphatase 2C 56 / AtPP2C56 / Protein phosphatase 2C ABI1 / PP2C ABI1 / Protein ABSCISIC ACID-INSENSITIVE 1


Mass: 35168.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ABI1, At4g26080, F20B18.190 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P49597, protein-serine/threonine phosphatase
#3: Chemical ChemComp-PYV / 4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide / Pyrabactin


Mass: 377.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13BrN2O2S / Comment: hormone*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M ammonium sulphate, 0.1M BisTris, 22% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. all: 50236 / Num. obs: 46283 / % possible obs: 92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 49.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KDJ

3kdj


Resolution: 2.15→29.62 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 15.115 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24751 3617 7.2 %RANDOM
Rwork0.2103 ---
obs0.21301 46283 96.99 %-
all-50236 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.935 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å2-1.47 Å2-2.38 Å2
2--0.11 Å21.22 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6956 0 48 180 7184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0227134
X-RAY DIFFRACTIONr_bond_other_d0.0030.024926
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.969649
X-RAY DIFFRACTIONr_angle_other_deg0.909311921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6775875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2823.253332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.062151228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2531568
X-RAY DIFFRACTIONr_chiral_restr0.0920.21076
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217905
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021487
X-RAY DIFFRACTIONr_mcbond_it1.8691.54405
X-RAY DIFFRACTIONr_mcbond_other0.7711.51782
X-RAY DIFFRACTIONr_mcangle_it3.30627114
X-RAY DIFFRACTIONr_scbond_it3.63832729
X-RAY DIFFRACTIONr_scangle_it5.4254.52535
X-RAY DIFFRACTIONr_rigid_bond_restr2.702312060
X-RAY DIFFRACTIONr_sphericity_free14.8775184
X-RAY DIFFRACTIONr_sphericity_bonded5.583511926
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 280 -
Rwork0.311 3118 -
obs--90.35 %

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