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- PDB-3kdi: Structure of (+)-ABA bound PYL2 -

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Basic information

Entry
Database: PDB / ID: 3kdi
TitleStructure of (+)-ABA bound PYL2
ComponentsPutative uncharacterized protein At2g26040
KeywordsHORMONE RECEPTOR / ABA / PYL2
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-A8S / Abscisic acid receptor PYL2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.379 Å
AuthorsYin, P. / Fan, H. / Hao, Q. / Yuan, X. / Yan, N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structural insights into the mechanism of abscisic acid signaling by PYL proteins
Authors: Yin, P. / Fan, H. / Hao, Q. / Yuan, X. / Wu, D. / Pang, Y. / Yan, C. / Li, W. / Wang, J. / Yan, N.
History
DepositionOct 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 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_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative uncharacterized protein At2g26040
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5742
Polymers21,3101
Non-polymers2641
Water25214
1
A: Putative uncharacterized protein At2g26040
hetero molecules

A: Putative uncharacterized protein At2g26040
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1494
Polymers42,6202
Non-polymers5292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area1410 Å2
ΔGint-9 kcal/mol
Surface area17580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.922, 60.922, 253.382
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-195-

HOH

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Components

#1: Protein Putative uncharacterized protein At2g26040 / PYL2


Mass: 21309.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O80992
#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


Mass: 264.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.18 Å3/Da / Density % sol: 61.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1M sodium citrate tribasic, 100mM Tris, pH8.5, 79mM MEGA-8 (Octanoyl-N-methylglucamide), 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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.379→32.97 Å / Num. obs: 11603 / % possible obs: 95.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 65.15 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 27
Reflection shellResolution: 2.379→2.47 Å / Rmerge(I) obs: 0.842 / Mean I/σ(I) obs: 2.3 / % possible all: 97.6

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KDH

3kdh


Resolution: 2.379→32.97 Å / Occupancy max: 1 / Occupancy min: 0.85 / FOM work R set: 0.798 / SU ML: 0.42 / Isotropic thermal model: TLS / σ(F): 1.34 / Phase error: 25.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2813 548 4.72 %Random
Rwork0.2256 11051 --
obs0.2279 11599 96.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.548 Å2 / ksol: 0.392 e/Å3
Displacement parametersBiso max: 172.93 Å2 / Biso mean: 72.51 Å2 / Biso min: 40.93 Å2
Baniso -1Baniso -2Baniso -3
1-1.871 Å2-0 Å2-0 Å2
2--1.871 Å20 Å2
3----3.741 Å2
Refinement stepCycle: LAST / Resolution: 2.379→32.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 19 14 1466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081480
X-RAY DIFFRACTIONf_angle_d1.0872013
X-RAY DIFFRACTIONf_dihedral_angle_d18.454568
X-RAY DIFFRACTIONf_chiral_restr0.073233
X-RAY DIFFRACTIONf_plane_restr0.005258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3786-2.61790.34081380.27512704X-RAY DIFFRACTION98
2.6179-2.99650.32361360.24382735X-RAY DIFFRACTION98
2.9965-3.77440.26531350.19932780X-RAY DIFFRACTION97
3.7744-32.97270.26821390.21992832X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: -0.8065 Å / Origin y: 23.7398 Å / Origin z: 9.5054 Å
111213212223313233
T0.3037 Å20.0744 Å2-0.0138 Å2-0.713 Å2-0.1309 Å2--0.4771 Å2
L0.3661 °20.6808 °2-0.2797 °2-1.6547 °20.0346 °2--1.3533 °2
S0.1624 Å °0.2218 Å °0.1724 Å °0.1397 Å °-0.0485 Å °-0.0536 Å °0.0527 Å °0.1503 Å °-0.1239 Å °
Refinement TLS groupSelection details: resid 7:187

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