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- PDB-3k90: The Abscisic acid receptor PYR1 in complex with Abscisic Acid -

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Basic information

Entry
Database: PDB / ID: 3k90
TitleThe Abscisic acid receptor PYR1 in complex with Abscisic Acid
ComponentsPutative uncharacterized protein
KeywordsHORMONE RECEPTOR / HYDROLASE REGULATOR / GENE REGULATOR / HORMONE / PLANT PROTEIN / SIGNALING PROTEIN / START domain / Bet V I domain / Hormone-Receptor complex / Regulator of protein phosphatase type 2C
Function / homology
Function and homology information


positive regulation of response to water deprivation / regulation of protein serine/threonine phosphatase activity / plant-type vacuole membrane / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / ubiquitin-like protein ligase binding / signaling receptor activity / protein homodimerization activity ...positive regulation of response to water deprivation / regulation of protein serine/threonine phosphatase activity / plant-type vacuole membrane / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / ubiquitin-like protein ligase binding / signaling receptor activity / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Polyketide cyclase / dehydrase and lipid transport / 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 / ACETIC ACID / Abscisic acid receptor PYR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDupeux, F.D. / Santiago, J. / Rodriguez, P.L. / Marquez, J.A.
CitationJournal: Nature / Year: 2009
Title: The abscisic acid receptor PYR1 in complex with abscisic acid.
Authors: Santiago, J. / Dupeux, F. / Round, A. / Antoni, R. / Park, S.Y. / Jamin, M. / Cutler, S.R. / Rodriguez, P.L. / Marquez, J.A.
History
DepositionOct 15, 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 10, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / 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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,68610
Polymers86,8214
Non-polymers8656
Water9,908550
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-44 kcal/mol
Surface area32930 Å2
MethodPISA
2
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8275
Polymers43,4112
Non-polymers4163
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-14 kcal/mol
Surface area17800 Å2
MethodPISA
3
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8595
Polymers43,4112
Non-polymers4493
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-16 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.810, 61.280, 72.550
Angle α, β, γ (deg.)105.65, 102.23, 89.91
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative uncharacterized protein / PYR1 / Putative uncharacterized protein AT4g17870 / Putative uncharacterized protein T6K21.50


Mass: 21705.340 Da / Num. of mol.: 4 / Mutation: P2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT4g17870, T6K21.50 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: O49686
#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.: 2 / Source method: obtained synthetically / Formula: C15H20O4 / Comment: hormone*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium magnesium acetate, 0.1M sodium cacodylate pH 6.5, 18% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 6, 2009 / Details: mirrors
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 54557 / Num. obs: 50927 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.1 Å / % possible all: 86.9

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0072refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CNW

3cnw


Resolution: 2→24.67 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.109 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23394 2647 5 %RANDOM
Rwork0.20042 ---
obs0.20209 50927 100 %-
all-54577 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.418 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20.1 Å20.88 Å2
2---2.27 Å20.26 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 2→24.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5584 0 60 550 6194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225803
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9627870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5055710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.6223.258267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.333151005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4451552
X-RAY DIFFRACTIONr_chiral_restr0.1070.2902
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214360
X-RAY DIFFRACTIONr_mcbond_it0.7121.53562
X-RAY DIFFRACTIONr_mcangle_it1.33325796
X-RAY DIFFRACTIONr_scbond_it1.81632241
X-RAY DIFFRACTIONr_scangle_it2.9874.52074
LS refinement shellResolution: 2→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 273 -
Rwork0.229 3681 -
obs--86.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.57460.736-0.04074.0644-0.21871.85320.1701-0.20110.03630.098-0.19930.10510.06310.13940.02920.0494-0.01320.02730.0383-0.00150.028215.0187-21.212515.1652
21.6043-0.27140.0161.32790.18181.17580.00430.0042-0.04230.0671-0.0117-0.091-0.03220.01280.00740.0239-0.00240.01780.0123-0.01310.052719.71257.44597.0329
32.01650.6138-0.02591.8294-0.1111.3236-0.0423-0.0096-0.0448-0.1577-0.00990.1017-0.0584-0.02340.05220.03480.01250.00220.00690.00480.0434-0.58846.9912-16.7229
41.2060.0592-0.07922.6721-0.28442.3701-0.00630.1148-0.00620.0481-0.04580.12780.0092-0.0980.05210.0211-0.0030.00140.0159-0.00590.01924.0488-21.0508-25.7871
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C2 - 179
2X-RAY DIFFRACTION2A1 - 180
3X-RAY DIFFRACTION3B1 - 180
4X-RAY DIFFRACTION4D1 - 180

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