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- PDB-3nj0: X-ray crystal structure of the PYL2-pyrabactin A complex -

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Basic information

Entry
Database: PDB / ID: 3nj0
TitleX-ray crystal structure of the PYL2-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
DI(HYDROXYETHYL)ETHER / Chem-PYV / Abscisic acid receptor PYL2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 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 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Abscisic acid receptor PYL2
C: Abscisic acid receptor PYL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2139
Polymers64,7773
Non-polymers1,4366
Water5,657314
1
A: Abscisic acid receptor PYL2
B: Abscisic acid receptor PYL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0455
Polymers43,1842
Non-polymers8613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-13 kcal/mol
Surface area17570 Å2
MethodPISA
2
C: Abscisic acid receptor PYL2
hetero molecules

C: Abscisic acid receptor PYL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3358
Polymers43,1842
Non-polymers1,1516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area3180 Å2
ΔGint-10 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.542, 105.151, 187.231
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-191-

PEG

21C-217-

HOH

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Components

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


Mass: 21592.215 Da / Num. of mol.: 3
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.: 3 / Source method: obtained synthetically / Formula: C16H13BrN2O2S
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#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.: 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: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein solution 2 ul- 20 mM Tris, pH 7.5, Precipitant solution 2 ul- 180 mM magnesium acetate, 16% (w/v) PEG_8000, 100 mM sodium cacodylate, pH 5.5, Cryoprotectant- 20% (v/v) glycerol, ...Details: Protein solution 2 ul- 20 mM Tris, pH 7.5, Precipitant solution 2 ul- 180 mM magnesium acetate, 16% (w/v) PEG_8000, 100 mM sodium cacodylate, pH 5.5, Cryoprotectant- 20% (v/v) glycerol, vapor diffusion, hanging drop, temperature 293K

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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: Dec 17, 2009 / 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: 1.89→50 Å / Num. obs: 48387 / % possible obs: 97.1 % / Redundancy: 7.2 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.151 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.89-1.923.60.46817480.91971.4
1.92-1.964.60.42420360.90882.4
1.96-25.50.36722450.93592.2
2-2.046.20.33324591.03398.1
2.04-2.0870.28624130.99299.8
2.08-2.137.50.27224721.013100
2.13-2.187.70.23424911.023100
2.18-2.247.70.19624741.085100
2.24-2.317.70.16924441.117100
2.31-2.387.70.15424841.221100
2.38-2.477.70.14124851.368100
2.47-2.577.70.12824901.315100
2.57-2.687.80.1124641.22299.9
2.68-2.827.70.08925041.334100
2.82-37.70.07724821.299100
3-3.237.70.07625171.321100
3.23-3.567.70.07924891.26199.7
3.56-4.077.80.06225311.17299.6
4.07-5.137.60.04725161.04598.3
5.13-507.60.03926430.99799.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å46.81 Å
Translation2.5 Å46.81 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 / Resolution: 1.89→29.66 Å / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.8693 / SU ML: 0.24 / σ(F): 0.13 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2047 1899 4.06 %
Rwork0.178 --
obs0.179 46723 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.344 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 143.04 Å2 / Biso mean: 39.2528 Å2 / Biso min: 15.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.4431 Å2-0 Å20 Å2
2---2.3881 Å2-0 Å2
3---3.8312 Å2
Refinement stepCycle: LAST / Resolution: 1.89→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4216 0 86 314 4616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014680
X-RAY DIFFRACTIONf_angle_d1.1786370
X-RAY DIFFRACTIONf_chiral_restr0.082712
X-RAY DIFFRACTIONf_plane_restr0.005794
X-RAY DIFFRACTIONf_dihedral_angle_d20.2991685
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8901-1.93730.279960.22362096219263
1.9373-1.98970.25411250.20332727285281
1.9897-2.04820.19781350.19013057319291
2.0482-2.11430.23711410.18143204334595
2.1143-2.18990.22791340.17773261339596
2.1899-2.27750.22371370.17123262339997
2.2775-2.38110.23691340.17443309344398
2.3811-2.50660.21851310.17913336346798
2.5066-2.66350.20091390.19433360349999
2.6635-2.8690.24061440.19333379352399
2.869-3.15750.21951420.18853401354399
3.1575-3.61370.21831460.166534373583100
3.6137-4.55020.14221430.14913422356599
4.5502-29.66360.18141520.17493573372599
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)
11.7569-0.04020.32371.27440.0290.94870.01870.04690.0292-0.06520.0171-0.05960.02740.0713-0.03640.1208-0.02020.02530.1564-0.03030.153912.4289-28.1016-10.1511
20.9241-0.0908-0.20421.78140.15541.17620.0337-0.0246-0.07450.06520.03560.01450.02770.0288-0.0670.2066-0.0002-0.04710.1453-0.01470.18780.4136-50.8639-21.095
31.6197-0.47130.00481.2868-0.2021.40450.11110.1239-0.0685-0.12620.008-0.06240.05140.126-0.10130.17290.0521-0.06090.1896-0.06630.1736-18.4832-26.7157-40.9782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A)A0
2X-RAY DIFFRACTION2(chain B)B0
3X-RAY DIFFRACTION3(chain C)C0

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