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- PDB-7avw: X-RAY CRYSTAL STRUCTURE OF THE CsPYL1-iSB07-HAB1 TERNARY COMPLEX -

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Basic information

Entry
Database: PDB / ID: 7avw
TitleX-RAY CRYSTAL STRUCTURE OF THE CsPYL1-iSB07-HAB1 TERNARY COMPLEX
Components
  • CsPYL1
  • Protein phosphatase 2C 16
KeywordsPLANT PROTEIN / CsPYL1 / HAB1 / Phosphatase ABA receptor inhibitor complex
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / signaling receptor activity / nucleus / metal ion binding / 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-S5N / 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: 2.1 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: To Be Published
Title: X-RAY CRYSTAL STRUCTURE OF THE CsPYL1-Lig2-HAB1 TERNARY COMPLEX
Authors: Albert, A. / Infantes, L. / Benavente, J.L.
History
DepositionNov 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Feb 28, 2024Group: Structure summary / Category: struct / Item: _struct.title

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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)61,30614
Polymers60,3252
Non-polymers98012
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-71 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.118, 62.450, 187.578
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 BL21(DE3) (bacteria) / References: UniProt: A0A067E666
#2: Protein Protein phosphatase 2C 16 / AtPP2C16 / AtP2C-HA / Protein HYPERSENSITIVE TO ABA 1 / Protein phosphatase 2C HAB1 / PP2C HAB1


Mass: 37031.445 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 BL21(DE3) (bacteria)
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase

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Non-polymers , 5 types, 191 molecules

#3: Chemical ChemComp-S5N / N-((1,4-dimethyl-2-oxo-1,2-dihydroquinolin-6-yl)methyl)benzenesulfonamide / ~{N}-[(1,4-dimethyl-2-oxidanylidene-quinolin-6-yl)methyl]benzenesulfonamide;


Mass: 342.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6.5 / Details: 0.5M CaCl2, 0.1M Mes pH6.5, 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: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.1→46.89 Å / Num. obs: 55897 / % possible obs: 99.3 % / Redundancy: 5.4 % / Biso Wilson estimate: 36.63 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.046 / Rrim(I) all: 0.11 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
4.44-6.2521.1537630.9960.055196.6
3.63-4.4418.1248200.9960.064196.5
3.15-3.6311.9558140.9940.093197.9
2.82-3.156.8765850.9850.159198.2
2.57-2.824.2173850.9670.255199
2.38-2.572.6379410.9420.393198.7
2.23-2.381.8585770.9070.549199
2.1-2.231.2889230.8010.802196.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5mn0

5mn0


Resolution: 2.1→46.89 Å / SU ML: 0.2534 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.824
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2511 1486 4.92 %
Rwork0.1955 28701 -
obs0.1982 30187 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.53 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3860 0 50 179 4089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773972
X-RAY DIFFRACTIONf_angle_d0.84685371
X-RAY DIFFRACTIONf_chiral_restr0.0543600
X-RAY DIFFRACTIONf_plane_restr0.0079718
X-RAY DIFFRACTIONf_dihedral_angle_d6.8858560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.37221220.30312493X-RAY DIFFRACTION94.4
2.17-2.250.34851380.26832527X-RAY DIFFRACTION99.11
2.25-2.340.28261370.24662539X-RAY DIFFRACTION99.18
2.34-2.440.28891510.23812585X-RAY DIFFRACTION99.24
2.44-2.570.31561410.23372571X-RAY DIFFRACTION99.38
2.57-2.730.29281340.2222614X-RAY DIFFRACTION99.42
2.73-2.940.29691230.21192615X-RAY DIFFRACTION99.82
2.94-3.240.25681340.2062614X-RAY DIFFRACTION99.53
3.24-3.710.26471140.17472659X-RAY DIFFRACTION99.32
3.71-4.670.19221440.15812674X-RAY DIFFRACTION99.47
4.67-46.890.22121480.17922810X-RAY DIFFRACTION98.9
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)
11.457233228530.655061966540.9227928782171.26704482841-0.4320404775711.483121368040.143718532305-0.234337617882-0.2533997778070.546557146149-0.209488510429-0.1598599681290.2724046548140.1903641266760.004957690610660.7070852045230.0464876972168-0.09059803914060.4337879042680.06379753429270.4168534811588.753111856126.3443973647551.3634433603
21.88791775228-0.127037972971-0.9928312158262.55023351003-0.63178007783.523621367070.0911611498661-0.094042712239-0.1430870739320.3389747770450.004673548998940.3353954731750.513894330245-0.306535909152-0.1127880124550.560372211156-0.0889949907242-0.01168727287620.3258092242430.02418814397050.343296576977-6.941925842881.9837525435838.4168576265
33.714061941560.616844888575-0.3442174627622.48169874861-0.8535520038372.287320782430.14775709062-0.06356494245520.05023280177820.427039668964-0.0632398043481-0.02691706260950.405488632198-0.0722899970882-0.08652692189250.6116962578630.0194400644307-0.07143526715530.3049146702740.01721097335830.3247861120193.687392241226.5693182818743.2523253695
42.81138349558-1.34995889529-4.001296320013.999453060911.273721176775.522355586220.184669708002-0.09182400253231.068418758760.5208290571660.125175412049-0.2995432902280.0438891301510.218196439336-0.3058858381630.52719237749-0.0029602637261-0.05285940344730.3539382932060.00448366828110.3595645849061.2200961687914.019924510839.8023663169
51.209654863180.276563761319-0.6282174707544.04756312458-0.255495678842.684265408710.080393901204-0.09567427210180.0915565766278-0.001889914248520.0195813638870.312866062691-0.34700869017-0.0019169605937-0.1197552373770.2280277593940.01636967315390.01850362383560.327270861956-0.02572540051250.320397746526-7.1345956169527.50188227435.73300755033
61.838620661091.87831179506-0.9521755051365.53780380818-3.057334651563.190731213950.0421028786670.06056831856740.5690458578920.4518935049790.3282637166430.752286904193-0.7625444641010.0315725214583-0.2512381859720.48345234860.006438172012090.02784701533440.399730815594-0.02209916770460.434459863172-3.8564633026939.41118670195.09957360091
73.179096504231.56322833221-0.06411327682686.11955307745-1.173222368023.82883210012-0.00861860000610.08190043291260.3177394267040.3169258565860.135936737917-0.183186459033-0.7902429761670.0100273887691-0.1437711244170.4943742387020.01847876058540.04045144157450.358538446714-0.05811123999170.372873007808-5.3784859676537.644972663816.8377154037
80.602463113781-0.3244266777610.2765360843781.49692268479-0.2051354461363.11605718662-0.0339340232558-0.1190358720440.03878305810770.2048841526730.0342127126851-0.0600840633087-0.1875825643290.0237964547483-0.003981202542490.265724091697-0.02870446852890.002361187075180.3323781959310.003466442485350.3131518586534.4841446658926.046701690312.1895199454
91.98802686423-0.199475618164-0.07509997725153.48799075135-0.1787504999972.48428708896-0.1149494074540.0371620545270.0353831677092-0.5649134358890.1273395961830.3166654906190.00179157654506-0.21220563018-0.1020377318320.219551615016-0.021664511541-0.01143946143110.31497798755-0.004801856710330.297973119404-3.4792186546121.5754753042-4.33487569432
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 21 through 67 )AA21 - 671 - 47
22chain 'A' and (resid 68 through 141 )AA68 - 14148 - 121
33chain 'A' and (resid 142 through 181 )AA142 - 181122 - 161
44chain 'A' and (resid 182 through 208 )AA182 - 208162 - 188
55chain 'B' and (resid 186 through 219 )BC186 - 2191 - 34
66chain 'B' and (resid 220 through 248 )BC220 - 24835 - 61
77chain 'B' and (resid 249 through 302 )BC249 - 30262 - 109
88chain 'B' and (resid 303 through 458 )BC303 - 458110 - 260
99chain 'B' and (resid 459 through 505 )BC459 - 505261 - 307

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