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- PDB-5moa: ABA RECEPTOR FROM TOMATO, SlPYL1 -

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Basic information

Entry
Database: PDB / ID: 5moa
TitleABA RECEPTOR FROM TOMATO, SlPYL1
ComponentsSlPYL1
KeywordsSIGNALING PROTEIN / ABA / RECEPTOR / SIGNALING / STRESS
Function / homologySTART domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMoreno-Alvero, M. / Yunta, C. / Gonzalez-Guzman, M. / Arbona, V. / Granell, A. / Martinez-Ripoll, M. / Infantes, L. / Rodriguez, P.L. / Albert, A.
CitationJournal: Mol Plant / Year: 2017
Title: Structure of Ligand-Bound Intermediates of Crop ABA Receptors Highlights PP2C as Necessary ABA Co-receptor.
Authors: Moreno-Alvero, M. / Yunta, C. / Gonzalez-Guzman, M. / Lozano-Juste, J. / Benavente, J.L. / Arbona, V. / Menendez, M. / Martinez-Ripoll, M. / Infantes, L. / Gomez-Cadenas, A. / Rodriguez, P.L. / Albert, A.
History
DepositionDec 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SlPYL1


Theoretical massNumber of molelcules
Total (without water)25,7381
Polymers25,7381
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.493, 89.493, 51.941
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SlPYL1


Mass: 25738.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Production host: Escherichia coli (E. coli) / References: UniProt: K4CN56
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7 / Details: 3.5 M de sulfato de amonio pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.65→43.15 Å / Num. obs: 281445 / % possible obs: 96.5 % / Redundancy: 7.5 % / CC1/2: 1 / Net I/σ(I): 26.5
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 7.7 % / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
Aimlessv7.0data scaling
SCALAv7.0data scaling
MOLREPv7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→43.147 Å / SU ML: 0.55 / Cross valid method: NONE / σ(F): 1.02 / Phase error: 28.98
RfactorNum. reflection% reflection
Rfree0.231 2732 5.06 %
Rwork0.214 --
obs0.2148 54003 96.46 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Bsol: 40.417 Å2 / ksol: 0.374 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.4387 Å2-0 Å20 Å2
2---5.4387 Å2-0 Å2
3---10.8773 Å2
Refinement stepCycle: LAST / Resolution: 1.65→43.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1515 0 0 151 1666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071546
X-RAY DIFFRACTIONf_angle_d1.0832105
X-RAY DIFFRACTIONf_dihedral_angle_d14.718561
X-RAY DIFFRACTIONf_chiral_restr0.068249
X-RAY DIFFRACTIONf_plane_restr0.005271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6502-1.67860.44871270.43952543X-RAY DIFFRACTION96
1.6786-1.70910.4631430.41162624X-RAY DIFFRACTION100
1.7091-1.7420.41181540.3762694X-RAY DIFFRACTION100
1.742-1.77760.37661640.34422622X-RAY DIFFRACTION100
1.7776-1.81620.33431260.31432674X-RAY DIFFRACTION100
1.8162-1.85850.32591590.29052623X-RAY DIFFRACTION100
1.8585-1.9050.29271130.27132591X-RAY DIFFRACTION99
1.905-1.95650.3159900.27591789X-RAY DIFFRACTION97
1.9565-2.0140.25981450.23152620X-RAY DIFFRACTION100
2.014-2.0790.2361270.22172708X-RAY DIFFRACTION100
2.079-2.15330.23331340.21612661X-RAY DIFFRACTION100
2.1533-2.23950.24961370.2272257X-RAY DIFFRACTION99
2.2395-2.34150.24181150.23132269X-RAY DIFFRACTION98
2.3415-2.46490.21311380.20442690X-RAY DIFFRACTION100
2.4649-2.61930.24641270.2142631X-RAY DIFFRACTION100
2.6193-2.82150.22151560.21872670X-RAY DIFFRACTION100
2.8215-3.10540.2431680.21482632X-RAY DIFFRACTION100
3.1054-3.55460.18061400.19182659X-RAY DIFFRACTION100
3.5546-4.47760.20371440.16772651X-RAY DIFFRACTION100
4.4776-43.16220.19421250.1922663X-RAY DIFFRACTION99

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