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- PDB-3nj1: X-ray crystal structure of the PYL2(V114I)-pyrabactin A complex -

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Basic information

Entry
Database: PDB / ID: 3nj1
TitleX-ray crystal structure of the PYL2(V114I)-pyrabactin A complex
ComponentsAbscisic acid receptor PYL2
KeywordsHORMONE RECEPTOR / START / ABA / PYR/PYL/RCAR / plant hormone / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / 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
N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide / Chem-PYV / Abscisic acid receptor PYL2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.948 Å
AuthorsPeterson, F.C. / Burgie, E.S. / Bingman, C.A. / Volkman, B.F. / Phillips Jr., G.N. / Cutler, S.R. / Jensen, D.R. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural basis for selective activation of ABA receptors.
Authors: Peterson, F.C. / Burgie, E.S. / Park, S.Y. / Jensen, D.R. / Weiner, J.J. / Bingman, C.A. / Chang, C.E. / Cutler, S.R. / Phillips, G.N. / Volkman, B.F.
History
DepositionJun 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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: Abscisic acid receptor PYL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3744
Polymers21,6061
Non-polymers7683
Water2,018112
1
A: Abscisic acid receptor PYL2
hetero molecules

A: Abscisic acid receptor PYL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7488
Polymers43,2122
Non-polymers1,5356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area2190 Å2
ΔGint-17 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.754, 61.754, 222.002
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-264-

HOH

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Components

#1: Protein Abscisic acid receptor PYL2 / PYR1-like protein 2 / Regulatory components of ABA receptor 14


Mass: 21606.240 Da / Num. of mol.: 1 / Mutation: V114I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Columbia / Gene: At2g26040, PYL2, RCAR14, T19L18.15 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O80992
#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
#3: Chemical ChemComp-P2M / N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide


Mass: 298.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14N2O2S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein solution 2 ul- 20 mM Tris, pH 7.5, Precipitant solution 2 ul- 220 mM ammonium citrate and 19.5% (w/v) PEG-3350, Cryoprotectant- 20% (v/v) glycerol, vapor diffusion, hanging drop, ...Details: Protein solution 2 ul- 20 mM Tris, pH 7.5, Precipitant solution 2 ul- 220 mM ammonium citrate and 19.5% (w/v) PEG-3350, Cryoprotectant- 20% (v/v) glycerol, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 3, 2010 / Details: 300 mm CCD
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 19119 / % possible obs: 98.6 % / Redundancy: 16.3 % / Biso Wilson estimate: 33.04 Å2 / Rmerge(I) obs: 0.068 / Χ2: 1.019 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.95-1.9860.6197780.68182.9
1.98-2.028.50.5348700.72793.9
2.02-2.0611.10.4789420.71198.3
2.06-2.1140.429110.76298.9
2.1-2.1515.90.3859360.74799.9
2.15-2.217.40.3319400.75699.9
2.2-2.2517.80.299370.78499.6
2.25-2.3117.90.2259460.83299.9
2.31-2.3817.70.2079660.836100
2.38-2.4618.30.1839360.916100
2.46-2.5418.10.1579451.058100
2.54-2.6518.40.1429631.13100
2.65-2.7718.30.129561.164100
2.77-2.9118.20.0919721.168100
2.91-3.1180.0719831.17899.8
3.1-3.3318.10.0639661.18799.9
3.33-3.6717.80.0589861.2199.7
3.67-4.217.50.04810051.25499.7
4.2-5.2916.60.03710291.21499.5
5.29-40170.03811521.30899.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å34.16 Å
Translation2.5 Å34.16 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.2.0phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NJ0

3nj0


Resolution: 1.948→30.428 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8538 / SU ML: 0.24 / σ(F): 0.14 / Phase error: 20.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 1816 9.89 %
Rwork0.1952 --
obs0.1974 18358 95.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.792 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso max: 163.01 Å2 / Biso mean: 39.4602 Å2 / Biso min: 11 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.948→30.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 49 112 1604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171594
X-RAY DIFFRACTIONf_angle_d1.2632174
X-RAY DIFFRACTIONf_chiral_restr0.101245
X-RAY DIFFRACTIONf_plane_restr0.006280
X-RAY DIFFRACTIONf_dihedral_angle_d19.211596
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.948-2.00070.2902970.2504946104373
2.0007-2.05960.25671220.21761153127588
2.0596-2.1260.25711350.19551201133693
2.126-2.2020.22141350.18571252138795
2.202-2.29010.23341390.18751234137395
2.2901-2.39430.23981420.2021287142998
2.3943-2.52050.24921390.2031278141798
2.5205-2.67830.22971460.20271330147698
2.6783-2.8850.24981440.2061296144098
2.885-3.1750.2171480.21361336148499
3.175-3.63380.20121500.18471359150999
3.6338-4.57570.19381520.15971368152099
4.5757-30.43160.19011670.18921502166999
Refinement TLS params.Method: refined / Origin x: 3.8011 Å / Origin y: 25.5497 Å / Origin z: 9.0924 Å
111213212223313233
T0.0803 Å20.0229 Å2-0.0253 Å2-0.1485 Å2-0.0044 Å2--0.1187 Å2
L1.6041 °2-0.3715 °2-0.2759 °2-1.1602 °20.0022 °2--1.2041 °2
S0.0003 Å °-0.1138 Å °-0.0887 Å °0.0996 Å °0.0548 Å °-0.0839 Å °0.0711 Å °0.1574 Å °-0.0539 Å °
Refinement TLS groupSelection details: (chain A)

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