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

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Basic information

Entry
Database: PDB / ID: 5mob
TitleABA RECEPTOR FROM TOMATO, SlPYL1
ComponentsSlPYL1_ABA
KeywordsSIGNALING PROTEIN / ABA / RECEPTOR / SIGNALING / STRESS
Function / homologySTART domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / 2-Layer Sandwich / Alpha Beta / Chem-A8S / :
Function and homology information
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.669 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 1.2Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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_ABA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0993
Polymers25,7381
Non-polymers3602
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area10190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.470, 87.470, 55.751
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_ABA


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: Chemical ChemComp-A8S / (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid / (+)-abscisic acid / (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexen-1-yl]-3-methyl-2,4-pentadienoic acid


Mass: 264.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20O4 / Comment: hormone*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
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: ADSC QUANTUM 210 / Detector: CCD / 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: 1.67→28.63 Å / Num. obs: 27365 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC1/2: 0.99 / Net I/σ(I): 17.1
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 6.1 % / % possible all: 100

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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: 1.669→28.631 Å / SU ML: 0.41 / Cross valid method: NONE / σ(F): 0.69 / Phase error: 27.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 2827 5.11 %
Rwork0.1914 --
obs0.193 55376 99.83 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.757 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.797 Å20 Å20 Å2
2---9.797 Å2-0 Å2
3---19.5941 Å2
Refinement stepCycle: LAST / Resolution: 1.669→28.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 24 168 1711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061575
X-RAY DIFFRACTIONf_angle_d1.0012147
X-RAY DIFFRACTIONf_dihedral_angle_d16.878578
X-RAY DIFFRACTIONf_chiral_restr0.064249
X-RAY DIFFRACTIONf_plane_restr0.005275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6691-1.69790.38451590.37162585X-RAY DIFFRACTION99
1.6979-1.72880.37021270.35412654X-RAY DIFFRACTION100
1.7288-1.7620.33791400.32532610X-RAY DIFFRACTION100
1.762-1.7980.30591580.28652613X-RAY DIFFRACTION100
1.798-1.83710.28121270.25132650X-RAY DIFFRACTION100
1.8371-1.87980.27671250.24042643X-RAY DIFFRACTION100
1.8798-1.92680.29781740.2432593X-RAY DIFFRACTION100
1.9268-1.97890.22491390.1952626X-RAY DIFFRACTION100
1.9789-2.03710.25011310.17532656X-RAY DIFFRACTION100
2.0371-2.10280.22011300.17652620X-RAY DIFFRACTION100
2.1028-2.1780.21021610.18382637X-RAY DIFFRACTION100
2.178-2.26510.2441250.20062636X-RAY DIFFRACTION100
2.2651-2.36820.21981530.1782601X-RAY DIFFRACTION100
2.3682-2.4930.23281530.18182628X-RAY DIFFRACTION100
2.493-2.64910.25311360.19522668X-RAY DIFFRACTION100
2.6491-2.85340.25021320.19452619X-RAY DIFFRACTION100
2.8534-3.14030.24021530.19282640X-RAY DIFFRACTION100
3.1403-3.59390.20171590.18352587X-RAY DIFFRACTION100
3.5939-4.52510.16731340.14922656X-RAY DIFFRACTION100
4.5251-28.63540.17141110.17882627X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 25.5726 Å / Origin y: 15.1959 Å / Origin z: 3.8631 Å
111213212223313233
T0.2023 Å2-0.0004 Å2-0.0248 Å2-0.1982 Å2-0.0069 Å2--0.2043 Å2
L1.5786 °2-0.1065 °20.0134 °2-0.9748 °2-0.2317 °2--0.896 °2
S0.042 Å °-0.0139 Å °-0.1412 Å °-0.0148 Å °0.034 Å °0.0259 Å °0.0214 Å °0.007 Å °0.0004 Å °
Refinement TLS groupSelection details: all

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