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- PDB-3nmh: Crystal structure of the abscisic receptor PYL2 in complex with p... -

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Basic information

Entry
Database: PDB / ID: 3nmh
TitleCrystal structure of the abscisic receptor PYL2 in complex with pyrabactin
ComponentsAbscisic acid receptor PYL2
Keywordshormone binding protein / PYL2 / Pyrabactin / Plant hormone receptor / helix-grip fold / hormone binding / abscisic acid
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
Chem-PYV / Abscisic acid receptor PYL2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsZhou, X.E. / Melcher, K. / Ng, L.-M. / Soon, F.-F. / Xu, Y. / Suino-Powell, K.M. / Kovach, A. / Li, J. / Yong, E.-L. / Xu, H.E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Identification and mechanism of ABA receptor antagonism.
Authors: Melcher, K. / Xu, Y. / Ng, L.M. / Zhou, X.E. / Soon, F.F. / Chinnusamy, V. / Suino-Powell, K.M. / Kovach, A. / Tham, F.S. / Cutler, S.R. / Li, J. / Yong, E.L. / Zhu, J.K. / Xu, H.E.
History
DepositionJun 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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
B: Abscisic acid receptor PYL2
C: Abscisic acid receptor PYL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6708
Polymers60,0623
Non-polymers1,6085
Water5,891327
1
A: Abscisic acid receptor PYL2
B: Abscisic acid receptor PYL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2726
Polymers40,0412
Non-polymers1,2314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-1 kcal/mol
Surface area17060 Å2
MethodPISA
2
C: Abscisic acid receptor PYL2
hetero molecules

C: Abscisic acid receptor PYL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7964
Polymers40,0412
Non-polymers7552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_354-x-2,y,-z-1/21
Buried area1890 Å2
ΔGint-14 kcal/mol
Surface area17550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.268, 105.074, 185.076
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 20020.504 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL2, RCAR14, At2g26040, T19L18.15 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M ammonium sulfate, 0.1M HEPES, 10 % glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 47822 / Num. obs: 51071 / % possible obs: 93.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 32.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KB0

3kb0


Resolution: 1.85→29.51 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.648 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23479 3668 7.3 %RANDOM
Rwork0.19449 ---
obs0.19736 46913 96.99 %-
all-52150 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.201 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å20 Å2
2--1.31 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4193 0 96 327 4616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224379
X-RAY DIFFRACTIONr_bond_other_d0.0010.022963
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9815952
X-RAY DIFFRACTIONr_angle_other_deg0.93737224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.815526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9823.819199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03315739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8371533
X-RAY DIFFRACTIONr_chiral_restr0.0990.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214772
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02877
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.921.52642
X-RAY DIFFRACTIONr_mcbond_other0.6151.51055
X-RAY DIFFRACTIONr_mcangle_it3.26224340
X-RAY DIFFRACTIONr_scbond_it3.54931737
X-RAY DIFFRACTIONr_scangle_it5.4464.51612
X-RAY DIFFRACTIONr_rigid_bond_restr2.04537342
X-RAY DIFFRACTIONr_sphericity_free13.8615327
X-RAY DIFFRACTIONr_sphericity_bonded8.05557252
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 262 -
Rwork0.205 3241 -
obs--93.26 %

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