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- PDB-5ur6: PYR1 bound to the rationally designed agonist cyanabactin -

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Basic information

Entry
Database: PDB / ID: 5ur6
TitlePYR1 bound to the rationally designed agonist cyanabactin
ComponentsAbscisic acid receptor PYR1
KeywordsHORMONE RECEPTOR / PYR/PYL/RCAR / PYR1 / cyanabactin
Function / homology
Function and homology information


positive regulation of response to water deprivation / : / 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 / : / 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 / cytosol / cytoplasm
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-8KM / Abscisic acid receptor PYR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.631 Å
AuthorsPeterson, F.C. / Vaidya, A. / Jensen, D.R. / Volkman, B.F. / Cutler, S.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1258175 United States
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: A Rationally Designed Agonist Defines Subfamily IIIA Abscisic Acid Receptors As Critical Targets for Manipulating Transpiration.
Authors: Vaidya, A.S. / Peterson, F.C. / Yarmolinsky, D. / Merilo, E. / Verstraeten, I. / Park, S.Y. / Elzinga, D. / Kaundal, A. / Helander, J. / Lozano-Juste, J. / Otani, M. / Wu, K. / Jensen, D.R. ...Authors: Vaidya, A.S. / Peterson, F.C. / Yarmolinsky, D. / Merilo, E. / Verstraeten, I. / Park, S.Y. / Elzinga, D. / Kaundal, A. / Helander, J. / Lozano-Juste, J. / Otani, M. / Wu, K. / Jensen, D.R. / Kollist, H. / Volkman, B.F. / Cutler, S.R.
History
DepositionFeb 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Abscisic acid receptor PYR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6308
Polymers20,7271
Non-polymers9037
Water2,666148
1
A: Abscisic acid receptor PYR1
hetero molecules

A: Abscisic acid receptor PYR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,26016
Polymers41,4552
Non-polymers1,80614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3380 Å2
ΔGint-125 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.436, 88.222, 112.072
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-206-

SO4

21A-370-

HOH

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Components

#1: Protein Abscisic acid receptor PYR1 / ABI1-binding protein 6 / Protein PYRABACTIN RESISTANCE 1 / Regulatory components of ABA receptor 11


Mass: 20727.404 Da / Num. of mol.: 1 / Fragment: UNP residues 1-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYR1, ABIP6, RCAR11, At4g17870, T6K21.50 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[pREP4] / References: UniProt: O49686
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-8KM / N-(4-cyano-3-cyclopropylphenyl)-1-(4-methylphenyl)methanesulfonamide


Mass: 326.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N2O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 302 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-tris propane, 2 M ammonium sulphate. Cryoprotected in perfluoropolyether cryo-oil

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 25599 / % possible obs: 99.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.79 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Χ2: 1.475 / Net I/σ(I): 63
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.63-1.666.60.1170.9870.0490.1271.77100
1.66-1.696.80.1120.9910.0460.1211.792100
1.69-1.726.90.1050.9910.0430.1141.83100
1.72-1.766.90.0980.9930.040.1061.752100
1.76-1.796.90.0930.9930.0380.1011.781100
1.79-1.846.90.0870.9930.0360.0951.719100
1.84-1.8870.080.9950.0320.0871.47699.8
1.88-1.935.20.0820.9930.0380.0911.73199.5
1.93-1.996.90.0660.9970.0260.0711.491100
1.99-2.0570.0580.9970.0240.0631.27699.9
2.05-2.1370.0580.9970.0230.0621.50899.8
2.13-2.2170.0540.9980.0220.0591.36299.8
2.21-2.3150.0530.9960.0240.0581.39293.8
2.31-2.437.20.0520.9970.0210.0561.24399.9
2.43-2.597.30.0490.9980.020.0531.16799.7
2.59-2.797.20.0510.9960.0210.0551.19499.6
2.79-3.077.20.0570.9960.0230.0621.1799.7
3.07-3.517.10.0590.9970.0240.0641.3298
3.51-4.425.60.0490.9970.0220.0541.394
4.42-5070.0430.9980.0180.0461.33898.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.63 Å34.66 Å
Translation1.63 Å34.66 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000708cdata collection
HKL-2000708cdata scaling
PHASER2.5.5phasing
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PYR1 (PDB ID 5UR4)

5ur4


Resolution: 1.631→34.66 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 2006 7.87 %Random
Rwork0.1869 23493 --
obs0.1894 25499 98.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.4 Å2 / Biso mean: 27.9941 Å2 / Biso min: 12.61 Å2
Refinement stepCycle: final / Resolution: 1.631→34.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 0 58 150 1602
Biso mean--40.07 32.97 -
Num. residues----173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051483
X-RAY DIFFRACTIONf_angle_d0.8132017
X-RAY DIFFRACTIONf_chiral_restr0.057226
X-RAY DIFFRACTIONf_plane_restr0.006251
X-RAY DIFFRACTIONf_dihedral_angle_d8.586892
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6313-1.67210.27911450.21251619176497
1.6721-1.71730.22431440.194516681812100
1.7173-1.76780.19061400.18431676181699
1.7678-1.82490.22231420.178116881830100
1.8249-1.89010.21881420.19031667180999
1.8901-1.96580.21861430.1931664180798
1.9658-2.05520.20821350.183916921827100
2.0552-2.16360.18691400.1817021842100
2.1636-2.29910.22311410.17721595173695
2.2991-2.47660.2091510.183216921843100
2.4766-2.72570.19781400.190316951835100
2.7257-3.11990.24791500.206417131863100
3.1199-3.92990.23411430.19261658180196
3.9299-34.66820.20971500.17431764191498
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)
15.14210.13441.2563.78545.75698.82030.30860.0666-0.56410.40690.0615-0.57310.7680.0724-0.33320.197-0.0063-0.05350.20660.03040.2221106.34828.385111.8421
22.9885-0.0192-0.54612.1146-1.2244.5277-0.041-0.92830.1870.7228-0.00490.0504-0.4322-0.12990.06750.31480.0679-0.02910.4144-0.00630.167198.128911.512421.5102
31.748-0.0906-1.07391.46641.03141.93610.10660.05850.1385-0.0173-0.07180.1055-0.142-0.1167-0.05280.1782-0.0017-0.02870.16850.00320.156385.174914.09137.3563
44.53710.45111.99112.57520.37722.9542-0.3130.34571.7502-0.38160.34670.9917-0.6972-0.3960.05370.36320.0212-0.04940.25760.1010.447280.785928.997611.2394
52.951.3128-0.56952.67560.521.77540.0099-0.18390.08590.1845-0.1220.24440.0835-0.01460.0990.15740.00580.00080.13760.0070.125985.17418.588416.9218
64.4714-3.30373.06839.28854.00278.24990.0803-0.2369-0.62380.63610.25660.510.1994-0.5976-0.25670.2497-0.01160.03950.22890.04420.167983.023714.04927.9351
75.0276-4.0259-5.80535.46786.13066.9262-0.02750.22350.0295-0.180.0786-0.28580.03670.0112-0.23590.1724-0.0289-0.00330.2158-0.00190.1852101.061911.59345.1197
81.0788-0.14370.07412.3340.54321.6745-0.1073-0.1358-0.00190.25620.10010.01010.8012-0.05410.20170.15410.0018-0.00080.17590.00850.141995.90229.189414.8918
91.85250.176-0.46073.3796-0.71516.3260.0438-0.1504-0.17540.303-0.0770.06580.28140.08790.0230.0999-0.0252-0.01780.10890.02230.193988.63544.824310.4006
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 20 )A2 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 38 )A21 - 38
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 66 )A39 - 66
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 77 )A67 - 77
5X-RAY DIFFRACTION5chain 'A' and (resid 78 through 112 )A78 - 112
6X-RAY DIFFRACTION6chain 'A' and (resid 113 through 120 )A113 - 120
7X-RAY DIFFRACTION7chain 'A' and (resid 121 through 133 )A121 - 133
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 155 )A134 - 155
9X-RAY DIFFRACTION9chain 'A' and (resid 156 through 181 )A156 - 181

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