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- PDB-9j6i: Crystal structure of the ABA receptor PYL1 in complex with DBSA c... -

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Basic information

Entry
Database: PDB / ID: 9j6i
TitleCrystal structure of the ABA receptor PYL1 in complex with DBSA compound
ComponentsAbscisic acid receptor PYL1
KeywordsLIPID BINDING PROTEIN / ABA receptor / PYL1
Function / homology
Function and homology information


protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / plastid / protein phosphatase inhibitor activity / defense response / signaling receptor activity / protein homodimerization activity / identical protein binding / nucleus ...protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / plastid / protein phosphatase inhibitor activity / defense response / 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-like domain superfamily
Similarity search - Domain/homology
: / Abscisic acid receptor PYL1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYan, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
Title: Stabilization of dimeric PYR/PYL/RCAR family members relieves abscisic acid-induced inhibition of seed germination.
Authors: Wang, Z.Z. / Cao, M.J. / Yan, J. / Dong, J. / Chen, M.X. / Yang, J.F. / Li, J.H. / Ying, R.N. / Gao, Y.Y. / Li, L. / Leng, Y.N. / Tian, Y. / Hewage, K.A.H. / Pei, R.J. / Huang, Z.Y. / Yin, P. ...Authors: Wang, Z.Z. / Cao, M.J. / Yan, J. / Dong, J. / Chen, M.X. / Yang, J.F. / Li, J.H. / Ying, R.N. / Gao, Y.Y. / Li, L. / Leng, Y.N. / Tian, Y. / Hewage, K.A.H. / Pei, R.J. / Huang, Z.Y. / Yin, P. / Zhu, J.K. / Hao, G.F. / Yang, G.F.
History
DepositionAug 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Abscisic acid receptor PYL1
B: Abscisic acid receptor PYL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0413
Polymers40,5532
Non-polymers4871
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-13 kcal/mol
Surface area16890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.990, 126.990, 60.195
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Abscisic acid receptor PYL1 / ABI1-binding protein 6 / PYR1-like protein 1 / Regulatory components of ABA receptor 9


Mass: 20276.693 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL1, RCAR12, At5g46790, MZA15.21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8VZS8
#2: Chemical ChemComp-H9X / 5-bromanyl-N2-[(4-bromophenyl)-bis(oxidanyl)-$l^4-sulfanyl]-N1,N1,N3,N3-tetrakis(oxidanyl)benzene-1,2,3-triamine


Mass: 487.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13Br2N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.46 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: PEG 8000, Potassium phosphate dibasic, Glycerol, Ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 25426 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 49.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.027 / Net I/σ(I): 13.35
Reflection shellResolution: 2.29→2.37 Å / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 2464 / CC1/2: 0.798

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Processing

Software
NameVersionClassification
PHENIX1.14rc3_3206refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KDJ

3kdj


Resolution: 2.3→43.68 Å / SU ML: 0.2819 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.2219 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2523 1271 5.15 %
Rwork0.2067 23402 -
obs0.209 24673 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 24 38 2784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872795
X-RAY DIFFRACTIONf_angle_d1.03483785
X-RAY DIFFRACTIONf_chiral_restr0.0556427
X-RAY DIFFRACTIONf_plane_restr0.0052492
X-RAY DIFFRACTIONf_dihedral_angle_d9.47571677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.30851130.25232560X-RAY DIFFRACTION98.38
2.39-2.50.32481410.25192586X-RAY DIFFRACTION99.85
2.5-2.630.32191480.24262565X-RAY DIFFRACTION99.96
2.63-2.80.31541370.23872593X-RAY DIFFRACTION99.93
2.8-3.020.26981500.23082599X-RAY DIFFRACTION99.89
3.02-3.320.28651620.22292571X-RAY DIFFRACTION99.96
3.32-3.80.26921380.2122631X-RAY DIFFRACTION99.93
3.8-4.790.22641310.17882621X-RAY DIFFRACTION99.93
4.79-43.680.2081510.19252676X-RAY DIFFRACTION99.58
Refinement TLS params.Method: refined / Origin x: -101.861271959 Å / Origin y: 78.1042889532 Å / Origin z: -2.19279726621 Å
111213212223313233
T0.352837620806 Å2-0.00522004308696 Å20.0327984516474 Å2-0.354255095273 Å2-0.0560097427178 Å2--0.463801793636 Å2
L3.2502197008 °2-0.539916855599 °20.594535188397 °2-2.30235506287 °2-0.220716323674 °2--0.979982945206 °2
S-0.0179115177475 Å °0.0793051684114 Å °0.142125666794 Å °0.0337520160059 Å °0.087541839371 Å °-0.215921482345 Å °-0.0634583603756 Å °0.236032266836 Å °-0.06361823237 Å °
Refinement TLS groupSelection details: all

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