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- PDB-6zuc: X-RAY CRYSTAL STRUCTURE OF THE CsPYL1-Lig1-HAB1 TERNARY COMPLEX -

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Basic information

Entry
Database: PDB / ID: 6zuc
TitleX-RAY CRYSTAL STRUCTURE OF THE CsPYL1-Lig1-HAB1 TERNARY COMPLEX
Components
  • CSPYL1
  • Protein phosphatase 2C 16
KeywordsPLANT PROTEIN / CsPYL1 / HAB1 / Phosphatase ABA receptor inhibitor complex
Function / homology
Function and homology information


protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / signaling receptor activity / protein homodimerization activity / metal ion binding / nucleus ...protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / signaling receptor activity / protein homodimerization activity / metal ion binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / Protein phosphatase 2C / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily ...PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / Protein phosphatase 2C / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / : / START-like domain superfamily
Similarity search - Domain/homology
: / Chem-QPZ / Abscisic acid receptor PYL1 / Protein phosphatase 2C 16
Similarity search - Component
Biological speciesCitrus sinensis (sweet orange)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.37 Å
AuthorsAlbert, A. / Infantes, L. / Benavente, J.L.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)BIO2017-89523-R Spain
CitationJournal: Sci Adv / Year: 2023
Title: Structure-guided engineering of a receptor-agonist pair for inducible activation of the ABA adaptive response to drought.
Authors: Lozano-Juste, J. / Infantes, L. / Garcia-Maquilon, I. / Ruiz-Partida, R. / Merilo, E. / Benavente, J.L. / Velazquez-Campoy, A. / Coego, A. / Bono, M. / Forment, J. / Pampin, B. / Destito, P. ...Authors: Lozano-Juste, J. / Infantes, L. / Garcia-Maquilon, I. / Ruiz-Partida, R. / Merilo, E. / Benavente, J.L. / Velazquez-Campoy, A. / Coego, A. / Bono, M. / Forment, J. / Pampin, B. / Destito, P. / Monteiro, A. / Rodriguez, R. / Cruces, J. / Rodriguez, P.L. / Albert, A.
History
DepositionJul 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 21, 2024Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CSPYL1
B: Protein phosphatase 2C 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,61116
Polymers59,5602
Non-polymers1,05114
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-92 kcal/mol
Surface area21520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.959, 62.733, 186.926
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein CSPYL1


Mass: 23293.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrus sinensis (sweet orange) / Gene: CISIN_1g046151mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A067E666
#2: Protein Protein phosphatase 2C 16 / AtPP2C16 / AtP2C-HA / Protein HYPERSENSITIVE TO ABA 1 / Protein phosphatase 2C HAB1 / PP2C HAB1


Mass: 36266.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HAB1, P2C-HA, At1g72770, F28P22.4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase

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Non-polymers , 5 types, 131 molecules

#3: Chemical ChemComp-QPZ / 1,4-dimethyl-2-oxidanylidene-~{N}-(phenylmethyl)quinoline-6-sulfonamide


Mass: 342.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5 / Details: 30%PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 2.37→46.73 Å / Num. obs: 20948 / % possible obs: 98.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 44.67 Å2 / CC1/2: 0.992 / Net I/σ(I): 5.6
Reflection shellResolution: 2.37→2.46 Å / Redundancy: 4.4 % / Num. unique obs: 1899 / CC1/2: 0.778 / % possible all: 87.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5mn0

5mn0


Resolution: 2.37→46.73 Å / SU ML: 0.371 / Cross valid method: FREE R-VALUE / σ(F): 0.35 / Phase error: 26.5354
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2434 1939 5.01 %
Rwork0.1811 36743 -
obs0.1843 20948 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.34 Å2
Refinement stepCycle: LAST / Resolution: 2.37→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3811 0 52 117 3980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823922
X-RAY DIFFRACTIONf_angle_d0.97855303
X-RAY DIFFRACTIONf_chiral_restr0.0519593
X-RAY DIFFRACTIONf_plane_restr0.0051685
X-RAY DIFFRACTIONf_dihedral_angle_d22.19461437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.430.4341130.33022073X-RAY DIFFRACTION78.16
2.43-2.50.34141440.28572672X-RAY DIFFRACTION99.75
2.5-2.570.31661160.27642677X-RAY DIFFRACTION99.93
2.57-2.660.31831460.2632693X-RAY DIFFRACTION99.82
2.66-2.750.3341460.24742629X-RAY DIFFRACTION99.82
2.75-2.860.28291390.21532713X-RAY DIFFRACTION99.17
2.86-2.990.26651450.19812596X-RAY DIFFRACTION99.13
2.99-3.150.30651640.19052663X-RAY DIFFRACTION99.79
3.15-3.350.26351310.17992691X-RAY DIFFRACTION99.93
3.35-3.60.22551430.16142685X-RAY DIFFRACTION99.72
3.6-3.970.21511330.15022659X-RAY DIFFRACTION99.64
3.97-4.540.18421150.13992649X-RAY DIFFRACTION99.07
4.54-5.720.20721340.14582697X-RAY DIFFRACTION99.89
5.72-46.730.20681700.1782646X-RAY DIFFRACTION99.68
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)
11.76328942335-0.7483545267840.2087839431542.173861175730.003758496617081.24974179152-0.154057448166-0.512404589257-0.146913694920.4097473969140.177003043537-0.08288275404480.1628155486990.212718234229-0.06372477939620.552846441231-0.0266892656159-0.07627748392940.475170733540.05021995026320.3539945875118.787580827936.7041155415251.3026354074
21.40259194364-0.318151682994-1.142199896941.23008755919-0.7737455186732.33348043495-0.0836709014216-0.0775537553676-0.07451051786790.04159116100950.1684462062260.1461500045760.428639401795-0.309457568051-0.09805469619310.427171620542-0.0562766759249-0.05474715973840.3685829404330.01852371734130.32064390068-7.612105111152.6589703924638.1350343379
32.036562057950.6178770077160.5307139880771.313349700910.2764720541671.673977923720.0361397646722-0.0326793130587-0.1584476078870.2412710981350.0290867249210.117739923710.1542352835820.0568098815673-0.09557891395980.4760918033020.0459249725288-0.005232667902780.2837732836450.06370864747320.2953365054473.104230843155.5343022729642.496426521
47.22278508593-1.57798279594-2.786450256711.954430239940.5025911522162.652322541350.0575100408312-0.3028175689670.5725350538960.3441327193210.0586888351144-0.263748723693-0.1357586783740.191033919151-0.1189139370050.3739611206140.007009277114810.007976687451140.3335732222030.0254942638370.3332560793812.276691882313.894770818839.308425343
51.78093254049-0.0698769533462-0.2909473434981.551065142890.4889183875981.716514193410.09425586052070.003600406319860.230028470474-0.01752793984820.05239767739490.245446492077-0.2344124337860.0511749125392-0.107017481930.176838310817-0.006260205020540.009533619751570.27270625733-0.01753453664520.258301380818-5.6210995861131.3384934096.12075465016
61.965645672290.4180682166490.6798046965252.06973417332-0.594936375662.27117739747-0.109784106526-0.009642948296110.1052718698210.2441272173120.318348259346-0.267070706627-0.535470640147-0.0219022081564-0.2172326703030.397703591020.03343262688670.03010895872460.309766460488-0.07440636598890.355054514356-5.454711043437.823888566916.7049378339
70.4204803077390.1603884691720.2254207698721.77820811369-0.4882774246461.49526582050.00683759485654-0.111860299583-0.0564879393830.179032415050.1088987658940.185949478085-0.145081976699-0.0667056588224-0.03980340093230.27338956831-0.003403756492230.0009285143994140.311742681185-0.000490032887990.3493024485670.9597512841829.466897132214.0910596392
80.461542635307-0.706877700779-0.24492165322.72203316748-0.5620679340571.32959605071-0.0881915927401-0.009937704263560.0696741588181-0.033283831772-0.0283705567630.0767704764096-0.02111498658980.251088120910.1371264703820.306876117951-0.0556842591757-0.03499431502810.3803960496830.004497930728290.30033091314111.008883389821.608812487725.9955103253
90.529732715909-0.8490962493840.07780165611961.75225496186-0.1790701270461.212851702390.0401929132514-0.01484699389620.093560778869-0.00192469311132-0.1038520407050.0592118298799-0.2036396346490.05196671882810.03315550572190.187647915551-0.05224974547040.01085233821550.2768319287760.004362168704430.3103765573785.2572147294728.194840756410.3406210602
104.71966936319-0.5493622898174.205841847640.781890164321-1.223220850676.126365365620.3858955667640.002280007399940.149068750813-0.212958634704-0.113627381273-0.2015295554860.3687681169410.0191472124083-0.1982882354090.2701275554790.02998988640810.03494467533340.320712087991-0.027192353760.3566133557213.6631039751121.2092381629-10.2263329015
111.72475100387-0.072714447723-0.993459286121.994690428840.07430467522942.241455734520.06799308124950.2056868044610.0324370392778-0.436761428638-0.001867644485920.1636763035580.0857676195617-0.190163034301-0.06892409610630.240552550121-0.0130655816876-0.03117585773470.280677821175-0.01243707236070.334182497591-3.1321657948821.7488453955-4.41924294813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 67 )
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 133 )
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 181 )
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 207 )
5X-RAY DIFFRACTION5chain 'B' and (resid 186 through 248 )
6X-RAY DIFFRACTION6chain 'B' and (resid 249 through 301 )
7X-RAY DIFFRACTION7chain 'B' and (resid 302 through 368 )
8X-RAY DIFFRACTION8chain 'B' and (resid 369 through 402 )
9X-RAY DIFFRACTION9chain 'B' and (resid 403 through 439 )
10X-RAY DIFFRACTION10chain 'B' and (resid 440 through 458 )
11X-RAY DIFFRACTION11chain 'B' and (resid 459 through 505 )

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