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- PDB-5ur4: 1.5 A Crystal structure of PYR1 bound to Pyrabactin -

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Basic information

Entry
Database: PDB / ID: 5ur4
Title1.5 A Crystal structure of PYR1 bound to Pyrabactin
ComponentsAbscisic acid receptor PYR1
KeywordsHORMONE RECEPTOR / PYR/PYL/RCAR / PYR1 / Pyrabactiln
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-PYV / Abscisic acid receptor PYR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsPeterson, F.C. / 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: To Be Published
Title: 1.5 A Crystal structure of PYR1 bound to Pyrabactin
Authors: Peterson, F.C. / Cutler, S.R.
History
DepositionFeb 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / 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)21,5657
Polymers20,7271
Non-polymers8386
Water3,243180
1
A: Abscisic acid receptor PYR1
hetero molecules

A: Abscisic acid receptor PYR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,13014
Polymers41,4552
Non-polymers1,67512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.427, 98.427, 71.467
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-346-

HOH

21A-415-

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 / Production host: Escherichia coli (E. coli) / References: UniProt: O49686
#2: Chemical ChemComp-PYV / 4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide / Pyrabactin


Mass: 377.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13BrN2O2S / Comment: hormone*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 302 K / Method: vapor diffusion / pH: 7
Details: 17% PEG 2K-MME, 0.32 M tetramethyl ammonium chloride, and 0.1 M Bis-tris propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.91998 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91998 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 31769 / % possible obs: 99.4 % / Redundancy: 22.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 55.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-ID% possible all
4.13-5021.40.03376.41768198.9
3.27-4.1323.30.03583.91653199.9
2.86-3.2723.80.04768.616421100
2.6-2.86240.05857.41613199.9
2.41-2.624.20.06358.61606199.9
2.27-2.4124.20.06456.91607199.8
2.16-2.4724.30.06957.81590199.7
2.06-2.1624.30.08354.71570199.7
1.98-2.0624.40.146.71580199.6
1.92-1.9824.20.12637.81580199.4
1.86-1.9224.20.15930.11569199.6
1.8-1.86240.18423.61579199.4
1.75-1.823.580.20121.51554199.4
1.71-1.7523.70.247171548199.2
1.67-1.7123.30.30413.81564199.2
1.64-1.6722.80.35511.31541199
1.6-1.6421.90.384101569198.9
1.57-1.620.90.4219.11547198.7
1.55-1.57190.4797.31540199.2
1.52-1.5516.30.58451549199.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000708cdata reduction
HKL-2000708cdata scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PYR1 P88S (PDB ID 3NJO)

3njo


Resolution: 1.52→29.371 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 16.87
RfactorNum. reflection% reflectionSelection details
Rfree0.1869 1967 6.29 %Random
Rwork0.1655 ---
obs0.1668 31286 98.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.52→29.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1387 0 52 180 1619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061562
X-RAY DIFFRACTIONf_angle_d0.8072124
X-RAY DIFFRACTIONf_dihedral_angle_d12.895957
X-RAY DIFFRACTIONf_chiral_restr0.054233
X-RAY DIFFRACTIONf_plane_restr0.005275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5199-1.55790.21461320.19251937X-RAY DIFFRACTION93
1.5579-1.60010.21441370.16621996X-RAY DIFFRACTION95
1.6001-1.64710.21311330.17032024X-RAY DIFFRACTION97
1.6471-1.70030.18771340.16652024X-RAY DIFFRACTION96
1.7003-1.76110.19991340.17432056X-RAY DIFFRACTION98
1.7611-1.83160.17841380.16722059X-RAY DIFFRACTION98
1.8316-1.91490.19921410.17452067X-RAY DIFFRACTION98
1.9149-2.01580.17981420.1642108X-RAY DIFFRACTION99
2.0158-2.14210.18111430.15942115X-RAY DIFFRACTION100
2.1421-2.30740.19471410.15822114X-RAY DIFFRACTION100
2.3074-2.53950.15791460.16652145X-RAY DIFFRACTION100
2.5395-2.90670.1781440.17412159X-RAY DIFFRACTION100
2.9067-3.6610.17021470.14972193X-RAY DIFFRACTION100
3.661-29.37670.20821550.1712322X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -35.6804 Å / Origin y: -12.5224 Å / Origin z: 7.5829 Å
111213212223313233
T0.1049 Å20.0129 Å2-0.0143 Å2-0.0863 Å20.0085 Å2--0.0931 Å2
L1.2614 °2-0.4249 °2-0.3058 °2-1.5796 °20.0217 °2--1.7171 °2
S-0.0595 Å °-0.0805 Å °0.0034 Å °0.0693 Å °0.0071 Å °-0.1001 Å °0.0411 Å °0.1837 Å °0.0393 Å °
Refinement TLS groupSelection details: (chain A)

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