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- PDB-3jrs: Crystal structure of (+)-ABA-bound PYL1 -

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Basic information

Entry
Database: PDB / ID: 3jrs
TitleCrystal structure of (+)-ABA-bound PYL1
ComponentsPutative uncharacterized protein At5g46790
KeywordsHormone Receptor / Plant Hormone Receptor / Abscisic acid / PYL1
Function / homology
Function and homology information


protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / plastid / protein phosphatase inhibitor activity / defense response / signaling receptor activity / protein homodimerization activity / identical protein binding / nucleus ...protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / plastid / protein phosphatase inhibitor activity / defense response / 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 PYL1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsMiyazono, K. / Miyakawa, T. / Sawano, Y. / Kubota, K. / Tanokura, M.
CitationJournal: Nature / Year: 2009
Title: Structural basis of abscisic acid signalling
Authors: Miyazono, K. / Miyakawa, T. / Sawano, Y. / Kubota, K. / Kang, H.J. / Asano, A. / Miyauchi, Y. / Takahashi, M. / Zhi, Y. / Fujita, Y. / Yoshida, T. / Kodaira, K. / Yamaguchi-Shinozaki, K. / Tanokura, M.
History
DepositionSep 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein At5g46790
B: Putative uncharacterized protein At5g46790
C: Putative uncharacterized protein At5g46790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7056
Polymers71,9123
Non-polymers7933
Water5,657314
1
A: Putative uncharacterized protein At5g46790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2352
Polymers23,9711
Non-polymers2641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein At5g46790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2352
Polymers23,9711
Non-polymers2641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative uncharacterized protein At5g46790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2352
Polymers23,9711
Non-polymers2641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.730, 97.730, 135.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Putative uncharacterized protein At5g46790 / PYL1


Mass: 23970.598 Da / Num. of mol.: 3 / Fragment: UNP residues 8-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VZS8
#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.: 3 / Source method: obtained synthetically / Formula: C15H20O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M HEPES, pH 8.0, 24% PEG3350, 0.2 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
2951
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONPhoton Factory BL-5A20.97926, 0.97942, 0.96418
Detector
TypeIDDetector
ADSC QUANTUM 315r1CCD
ADSC QUANTUM 315r2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979261
30.979421
40.964181
ReflectionResolution: 2.05→20 Å / Num. obs: 41716 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.378 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 32.29
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.05-2.10.5166.24411330311,2100
2.1-2.160.4646.94328229751,2100
2.16-2.220.3558.94192828891,2100
2.22-2.290.27211.44049127841,2100
2.29-2.370.233133934627081,2100
2.37-2.450.19115.33853226581,2100
2.45-2.540.1618.33694425431,2100
2.54-2.650.12622.13568424641,2100
2.65-2.760.09827.13410323581,2100
2.76-2.90.08132.33232922401,2100
2.9-3.060.06538.23117621661,2100
3.06-3.240.05247.12919920401,2100
3.24-3.470.04156.62753119361,2100
3.47-3.740.03762.72538617951,2100
3.74-4.10.03271.12342716801,2100
4.1-4.580.03175.12083115171,2100
4.58-5.290.03175.91812913551,2100
5.29-6.480.0374.71562311681,2100
6.48-9.170.02579.9124249291,299.9
9.17-200.02179.657524801,285.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefmac_5.5.0088refinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.009 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2109 5.1 %RANDOM
Rwork0.19 ---
obs0.192 41713 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.47 Å2 / Biso mean: 24.221 Å2 / Biso min: 8.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 0 57 314 4475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0214230
X-RAY DIFFRACTIONr_angle_refined_deg2.3131.9565732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4015499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.63922.909220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68715728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2791550
X-RAY DIFFRACTIONr_chiral_restr0.1750.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213217
X-RAY DIFFRACTIONr_mcbond_it1.1961.52521
X-RAY DIFFRACTIONr_mcangle_it2.06724109
X-RAY DIFFRACTIONr_scbond_it3.33531709
X-RAY DIFFRACTIONr_scangle_it54.51623
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 140 -
Rwork0.211 2856 -
all-2996 -
obs--100 %
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)
12.0930.1894-0.93822.74070.42752.84850.0379-0.16240.064-0.08910.16240.0477-0.10670.3846-0.20020.0298-0.03210.0390.0706-0.03520.08329.347-11.77527.388
21.5766-0.09910.16092.30511.67543.69460.131-0.0851-0.0522-0.1127-0.13250.0775-0.032-0.09190.00140.0239-0.01490.00180.0445-0.00680.051159.667-4.57331.563
33.0507-0.79930.21272.12840.24341.54520.32970.31990.0026-0.367-0.3695-0.1281-0.08640.03740.03980.09250.08960.01430.09880.02270.025583.276-16.78717.483
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 209
2X-RAY DIFFRACTION1A1
3X-RAY DIFFRACTION2B30 - 209
4X-RAY DIFFRACTION2B2
5X-RAY DIFFRACTION3C38 - 209
6X-RAY DIFFRACTION3C3

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