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- PDB-5ur5: PYR1 bound to the rationally designed agonist 4m -

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Basic information

Entry
Database: PDB / ID: 5ur5
TitlePYR1 bound to the rationally designed agonist 4m
ComponentsAbscisic acid receptor PYR1
KeywordsHORMONE RECEPTOR / PYR/PYL/RCAR / PYR1 / agonist
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-8KP / Abscisic acid receptor PYR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 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 29, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: Abscisic acid receptor PYR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,00112
Polymers20,7271
Non-polymers1,27311
Water2,540141
1
A: Abscisic acid receptor PYR1
hetero molecules

A: Abscisic acid receptor PYR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,00124
Polymers41,4552
Non-polymers2,54622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4720 Å2
ΔGint-133 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.605, 88.220, 112.167
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-203-

SO4

21A-205-

SO4

31A-205-

SO4

41A-347-

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-8KP / N-(4-cyano-3-ethyl-5-methylphenyl)-1-(4-methylphenyl)methanesulfonamide


Mass: 328.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N2O2S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 302 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium acetate, 1.5 M ammonium sulfate. Cryoported in well solution plus 20% w/v glycerol

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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: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 15572 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 16.51 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.022 / Rrim(I) all: 0.059 / Χ2: 1.51 / Net I/σ(I): 28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.93-1.966.80.1350.9880.0550.1461.56599.5
1.96-270.1290.9910.0520.1391.612100
2-2.047.10.1150.9920.0460.1241.613100
2.04-2.0870.1090.9920.0440.1181.83100
2.08-2.127.20.1030.9940.0410.1111.748100
2.12-2.177.10.0980.9940.0390.1061.766100
2.17-2.237.20.0920.9940.0360.0991.74100
2.23-2.297.20.0860.9930.0340.0931.676100
2.29-2.367.20.0810.9960.0320.0871.629100
2.36-2.437.20.0780.9960.0310.0831.546100
2.43-2.527.20.070.9960.0280.0761.45100
2.52-2.627.30.070.9960.0280.0751.494100
2.62-2.747.30.0640.9970.0250.0691.47100
2.74-2.887.30.0560.9980.0220.061.365100
2.88-3.067.30.0530.9980.0210.0561.318100
3.06-3.37.30.0480.9980.0190.0521.225100
3.3-3.637.30.0430.9980.0170.0461.407100
3.63-4.167.30.0390.9980.0160.0421.269100
4.16-5.247.20.0380.9950.0150.0411.258100
5.24-506.90.0420.9980.0180.0451.29399.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.93 Å34.67 Å
Translation1.93 Å34.67 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: 1.93→34.671 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.186 1548 9.99 %Random selection
Rwork0.1534 13952 --
obs0.1566 15500 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.09 Å2 / Biso mean: 23.8723 Å2 / Biso min: 2.99 Å2
Refinement stepCycle: final / Resolution: 1.93→34.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 82 142 1626
Biso mean--38.48 30.63 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061504
X-RAY DIFFRACTIONf_angle_d0.7622036
X-RAY DIFFRACTIONf_chiral_restr0.057223
X-RAY DIFFRACTIONf_plane_restr0.005253
X-RAY DIFFRACTIONf_dihedral_angle_d9.259898
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9299-1.99220.24741390.17551222136198
1.9922-2.06340.17411360.14851240137699
2.0634-2.1460.21331490.14741237138699
2.146-2.24360.19711300.14621279140999
2.2436-2.36190.18371350.1571244137999
2.3619-2.50980.20151400.156212661406100
2.5098-2.70350.17291390.158812671406100
2.7035-2.97550.19331490.16212681417100
2.9755-3.40570.19551420.152312841426100
3.4057-4.28960.16751370.132412901427100
4.2896-34.67670.16951520.166213551507100
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)
13.41920.45670.59095.7086.53787.91870.074-0.10770.2365-0.50670.2399-0.9289-0.32940.3442-0.29490.0990.00330.03670.16840.00910.188723.7055-9.7892-11.5893
22.44820.50530.72492.36890.34897.90870.02040.5343-0.0629-0.50450.0301-0.09210.37990.3448-0.08960.19370.00990.04030.21090.00560.137314.6695-10.6406-21.5505
31.00250.19870.77632.84450.70872.04310.06230.0068-0.12090.0502-0.02460.1780.0815-0.1432-0.0440.0630.0070.03060.0867-0.0020.07081.7257-14.1124-7.3426
46.65540.6374-0.74822.01720.82865.9578-0.354-0.3546-1.46430.4690.36770.79190.9726-0.36490.05770.3066-0.05060.01690.15270.09050.3741-2.8411-28.9091-11.368
52.0192-0.09340.24021.48670.98421.48180.11410.2864-0.0826-0.2163-0.12880.192-0.057-0.03580.01150.0990.0070.00060.1187-0.01380.09051.2957-17.6341-19.2248
67.94563.93047.73815.54255.57348.2573-0.1106-0.29920.1580.2904-0.0288-0.0830.0426-0.0282-0.06890.10130.03860.00110.1630.00220.129617.5063-11.6756-5.1833
71.3754-0.31680.22361.79781.03942.82090.03590.20780.1369-0.2514-0.0689-0.0271-0.31450.04340.06730.08690.00180.00810.08910.02190.11167.9643-6.2698-14.0687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 20 )A5 - 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 120 )A78 - 120
6X-RAY DIFFRACTION6chain 'A' and (resid 121 through 133 )A121 - 133
7X-RAY DIFFRACTION7chain 'A' and (resid 134 through 181 )A134 - 181

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