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- PDB-3rt2: Crystal structure of apo-PYL10 -

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Basic information

Entry
Database: PDB / ID: 3rt2
TitleCrystal structure of apo-PYL10
ComponentsAbscisic acid receptor PYL10
KeywordsHYDROLASE INHIBITOR / PYL10 / ABA-independent PP2C inhibitor / PP2Cs / abscisic acid / ABA receptor
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / protein homodimerization activity / 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
Abscisic acid receptor PYL10
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHao, Q. / Yin, P. / Li, W. / Wang, L. / Yan, C. / Wang, J. / Yan, N.
CitationJournal: Mol.Cell / Year: 2011
Title: The Molecular Basis of ABA-Independent Inhibition of PP2Cs by a Subclass of PYL Proteins
Authors: Hao, Q. / Yin, P. / Li, W. / Wang, L. / Yan, C. / Lin, Z. / Wu, J.Z. / Wang, J. / Yan, S.F. / Yan, N.
History
DepositionMay 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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 PYL10


Theoretical massNumber of molelcules
Total (without water)20,6751
Polymers20,6751
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Abscisic acid receptor PYL10

A: Abscisic acid receptor PYL10


Theoretical massNumber of molelcules
Total (without water)41,3492
Polymers41,3492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area2000 Å2
ΔGint-12 kcal/mol
Surface area17110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.017, 98.425, 96.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-345-

HOH

21A-347-

HOH

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Components

#1: Protein Abscisic acid receptor PYL10 / ABI1-binding protein 8 / PYR1-like protein 10 / Regulatory components of ABA receptor 4


Mass: 20674.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8H1R0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 43.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M magnesium acetate, 20% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 21, 2010
RadiationMonochromator: rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 29479 / % possible obs: 99.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.04
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 5.48 / Num. unique all: 2918 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.3_473)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KDH

3kdh


Resolution: 1.5→28.598 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8697 / SU ML: 0.17 / σ(F): 0 / Phase error: 19.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 1455 5.07 %
Rwork0.1739 --
obs0.1755 28673 97.07 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.786 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 113.57 Å2 / Biso mean: 29.2402 Å2 / Biso min: 11.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.1913 Å20 Å2-0 Å2
2--0.1349 Å20 Å2
3----0.3255 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1353 0 0 175 1528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071493
X-RAY DIFFRACTIONf_angle_d1.0232033
X-RAY DIFFRACTIONf_chiral_restr0.064234
X-RAY DIFFRACTIONf_plane_restr0.004266
X-RAY DIFFRACTIONf_dihedral_angle_d14.853564
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5002-1.55380.27221280.20492508263690
1.5538-1.6160.24621480.18012578272694
1.616-1.68950.26081310.17082639277095
1.6895-1.77860.19071680.16192666283497
1.7786-1.890.22241330.14432756288998
1.89-2.03590.23731420.15432749289199
2.0359-2.24070.19221520.160227732925100
2.2407-2.56470.21151600.168627982958100
2.5647-3.23060.21291480.182828502998100
3.2306-28.60310.18321450.18352901304698

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