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- PDB-3r6p: Crystal structure of abscisic acid-bound PYL10 -

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Basic information

Entry
Database: PDB / ID: 3r6p
TitleCrystal structure of abscisic acid-bound PYL10
ComponentsAbscisic acid receptor PYL10
KeywordsHORMONE RECEPTOR / Arabidopsis Proteins Receptors / Abscisic Acid binding
Function / homology
Function and homology information


regulation of protein serine/threonine phosphatase activity / 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
Chem-A8S / Abscisic acid receptor PYL10
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSun, D.M. / Wu, M.H. / Wang, H.P. / Zang, J.Y. / Tian, C.L.
CitationJournal: To be Published
Title: Crystal structure of abscisic acid-bound PYL10
Authors: Sun, D.M. / Wu, M.H. / Wang, H.P. / Zang, J.Y. / Tian, C.L.
History
DepositionMar 22, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Abscisic acid receptor PYL10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0102
Polymers21,7461
Non-polymers2641
Water19811
1


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

A: Abscisic acid receptor PYL10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0204
Polymers43,4922
Non-polymers5292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area1350 Å2
ΔGint-15 kcal/mol
Surface area15410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.327, 68.327, 63.396
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: 21745.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL10 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8H1R0
#2: 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.: 1 / Source method: obtained synthetically / Formula: C15H20O4 / Comment: hormone*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 1.96 Å3/Da / Density % sol: 37.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG monoethyl ether 5000, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorDate: Mar 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 4929

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UQH

3uqh


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 480 9.8 %RANDOM
Rwork0.2389 4435 --
obs0.2428 4915 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.56 Å2 / Biso mean: 67.6368 Å2 / Biso min: 47.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20.85 Å20 Å2
2--1.7 Å20 Å2
3----2.55 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 19 11 1230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021247
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9821691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9195155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.04524.52853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00215230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.333158
X-RAY DIFFRACTIONr_chiral_restr0.0720.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021911
LS refinement shellResolution: 2.697→2.767 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 41 -
Rwork0.337 310 -
all-351 -
obs--99.43 %

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