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- PDB-5jnn: Crystal structure of abscisic acid receptor PYL2 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5jnn
TitleCrystal structure of abscisic acid receptor PYL2 in complex with Phaseic acid.
ComponentsAbscisic acid receptor PYL2
KeywordsSIGNALING PROTEIN / ABA receptor / Phaseic acid / PYR/PYL
Function / homology
Function and homology information


protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6LM / Abscisic acid receptor PYL2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWeng, J.K. / Noel, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2016
Title: Co-evolution of Hormone Metabolism and Signaling Networks Expands Plant Adaptive Plasticity.
Authors: Weng, J.K. / Ye, M. / Li, B. / Noel, J.P.
History
DepositionApr 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Abscisic acid receptor PYL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5922
Polymers21,3101
Non-polymers2821
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.950, 60.950, 255.812
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Abscisic acid receptor PYL2 / PYR1-like protein 2 / Regulatory components of ABA receptor 14


Mass: 21309.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL2, RCAR14, At2g26040, T19L18.15 / Production host: Escherichia coli (E. coli) / References: UniProt: O80992
#2: Chemical ChemComp-6LM / (3S,4E)-5-[(1R,5R,8S)-8-hydroxy-1,5-dimethyl-3-oxo-6-oxabicyclo[3.2.1]octan-8-yl]-3-methylpent-4-enoic acid


Mass: 282.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.19 Å3/Da / Density % sol: 61.4 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 4 M sodium formate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→52.784 Å / Num. obs: 13406 / % possible obs: 99.8 % / Redundancy: 2 % / Net I/σ(I): 23.57

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→52.78 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.33
RfactorNum. reflection% reflection
Rfree0.235 672 5.01 %
Rwork0.189 --
obs0.191 13405 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→52.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 20 52 1461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081438
X-RAY DIFFRACTIONf_angle_d1.1071959
X-RAY DIFFRACTIONf_dihedral_angle_d16.113540
X-RAY DIFFRACTIONf_chiral_restr0.075227
X-RAY DIFFRACTIONf_plane_restr0.004251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.47760.27361290.21192438X-RAY DIFFRACTION99
2.4776-2.7270.27461310.21252471X-RAY DIFFRACTION100
2.727-3.12150.27121320.21532513X-RAY DIFFRACTION100
3.1215-3.93260.2171340.18112551X-RAY DIFFRACTION100
3.9326-52.79810.22071460.17772760X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 0.5697 Å / Origin y: -24.6025 Å / Origin z: 9.0723 Å
111213212223313233
T0.2296 Å20.0297 Å20.0334 Å2-0.4402 Å20.0932 Å2--0.3235 Å2
L2.0729 °20.0954 °20.3842 °2-1.5751 °20.0955 °2--1.7263 °2
S0.0461 Å °0.1293 Å °0.0929 Å °0.1434 Å °0.1114 Å °0.1872 Å °-0.0287 Å °-0.2121 Å °-0.1061 Å °
Refinement TLS groupSelection details: ALL

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