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- PDB-8ay3: X-RAY CRYSTAL STRUCTURE OF THE CsPYL1-iSB9-HAB1 TERNARY COMPLEX -

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Basic information

Entry
Database: PDB / ID: 8ay3
TitleX-RAY CRYSTAL STRUCTURE OF THE CsPYL1-iSB9-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 / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / signaling receptor 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 / START-like domain superfamily
Similarity search - Domain/homology
: / Chem-OE3 / 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: 1.9 Å
AuthorsInfantes, L. / Albert, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities 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
DepositionSep 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)61,14614
Polymers60,2652
Non-polymers88112
Water2,972165
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-92 kcal/mol
Surface area21570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.702, 62.250, 187.014
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: 36971.438 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, 177 molecules

#3: Chemical ChemComp-OE3 / ~{N}-[(1-ethyl-4-methyl-2-oxidanylidene-quinolin-6-yl)methyl]benzenesulfonamide


Mass: 356.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N2O3S / 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 / Chloride


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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6.5 / Details: 30% PEG3350

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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 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 1.9→44.05 Å / Num. obs: 39950 / % possible obs: 98.92 % / Redundancy: 6.4 % / Biso Wilson estimate: 35.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09521 / Rrim(I) all: 0.104 / Net I/σ(I): 11.48
Reflection shellResolution: 1.9→1.968 Å / Rmerge(I) obs: 2.313 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3884 / CC1/2: 0.502 / CC star: 0.817 / Rrim(I) all: 2.525 / % possible all: 98.25

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Processing

Software
NameVersionClassification
XDS2019data reduction
XDS2019data scaling
PHENIX1.19.2-4158phasing
PHENIX1.19.2-4158refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5MN0
Resolution: 1.9→44.05 Å / SU ML: 0.2671 / Cross valid method: FREE R-VALUE / σ(F): 0.2 / Phase error: 29.4101
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2409 3663 4.9 %
Rwork0.1944 71146 -
obs0.1967 39950 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.86 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 41 165 4015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00843911
X-RAY DIFFRACTIONf_angle_d0.92945291
X-RAY DIFFRACTIONf_chiral_restr0.0599592
X-RAY DIFFRACTIONf_plane_restr0.0055708
X-RAY DIFFRACTIONf_dihedral_angle_d21.63781450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.39731490.39962461X-RAY DIFFRACTION88.59
1.92-1.950.41431550.36882720X-RAY DIFFRACTION97.76
1.95-1.980.37131200.3162768X-RAY DIFFRACTION98.63
1.98-2.010.35221250.30372748X-RAY DIFFRACTION98.39
2.01-2.040.34121470.28142804X-RAY DIFFRACTION98.47
2.04-2.070.43871220.30132651X-RAY DIFFRACTION96.82
2.07-2.110.35041410.29092726X-RAY DIFFRACTION97.62
2.11-2.140.31141230.24972814X-RAY DIFFRACTION98.33
2.14-2.190.28571290.2542696X-RAY DIFFRACTION98.81
2.19-2.230.27081700.25852793X-RAY DIFFRACTION98.41
2.23-2.280.39221550.29762602X-RAY DIFFRACTION95.04
2.28-2.330.28351470.24252735X-RAY DIFFRACTION98.7
2.33-2.390.28991470.22372805X-RAY DIFFRACTION99.23
2.39-2.450.28691420.21492733X-RAY DIFFRACTION99.1
2.45-2.530.2551280.21282803X-RAY DIFFRACTION98.55
2.53-2.610.25571340.20452726X-RAY DIFFRACTION98.79
2.61-2.70.24481580.20612774X-RAY DIFFRACTION98.85
2.7-2.810.27531380.20552773X-RAY DIFFRACTION99.49
2.81-2.940.25211320.19642771X-RAY DIFFRACTION99.11
2.94-3.090.25371420.18012772X-RAY DIFFRACTION99.28
3.09-3.290.18431520.17472778X-RAY DIFFRACTION99.49
3.29-3.540.23751210.15952745X-RAY DIFFRACTION98.49
3.54-3.890.1691400.14972744X-RAY DIFFRACTION97.73
3.9-4.460.23311480.15032702X-RAY DIFFRACTION97.24
4.46-5.610.18361510.16182742X-RAY DIFFRACTION99.11
5.62-44.050.21791470.18572760X-RAY DIFFRACTION98.88
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.00948934262-0.7635894706290.1453854957062.50141091303-0.1767306298161.079380856920.0329591022063-0.27814304712-0.1184277415620.6755428211540.0183825211212-0.3063203124150.3029153607390.283876889343-0.02716827581640.68543937105-0.0154279894495-0.1429046578520.4167779115030.05685369104360.4209343094458.66774835296.2618898294251.4072572235
21.274174003560.144262416923-0.7080847894931.43923811663-0.5370646920542.411073085870.05284022130430.0114304894674-0.09731431003660.1844141582110.08814525006520.3145345396010.547059198143-0.211562225461-0.1293929739580.492451220116-0.0366481313116-0.02094338753040.3129633030420.01829862863030.343312888881-6.836682465911.8678614535838.1878760377
32.101130192091.041510461110.352022253642.53795168069-0.01364448444622.487153955670.1957720923640.0532603307109-0.05288612960770.589730657426-0.164107347789-0.2072163730070.3634841309850.0175448975604-0.02492449201990.4983556206340.00890966306722-0.06898781055640.284086635210.05302718912790.3241348720453.633706178916.5527398665642.9734531369
46.011603748960.314117493655-2.460998516722.34723279150.08738784053452.821958501690.2534289309590.08347569209460.8165559120320.2029401740730.0884956647739-0.1983664421370.02740405865310.0908993637203-0.3563939770230.4453225230660.0174506164277-0.02241050099630.340541799497-0.005336930105730.3560178925391.9453812288113.646652191839.4162020047
55.28640433696-0.729607853962-0.7258975962165.807054016530.7198728976445.8051384793-0.024946931747-0.205676978390.6357011996890.08188955311770.06351392218650.00883983087565-0.6604446906750.3712067232260.0235824683730.3290731017840.0529801305177-0.04727183091230.322779075811-0.01356884707140.368846639874-7.0862949149932.6998474321-4.67625876925
61.708305848581.17130393073-0.7030052730693.76000927788-3.759313364346.07225146420.05842621002080.02339706098830.0853081215469-0.1727146453780.204192189939-0.1730957795370.2340725102160.210026751051-0.05778673225370.170094297340.00931234154024-0.00185095226340.2609934049770.01748362103230.287131281518-6.286784423318.01535600312.80941412417
74.57450612322-0.2471892760941.142451354984.74187506952-1.944276615348.90768451342-0.0348141456722-0.284970171723-0.4607640994620.7312976623780.287998930691-0.3845747676270.8030376945920.216545560769-0.06665463152010.3948227434180.0205378868699-0.02358940502280.2875981606330.04379390772440.366098581612-4.638739520527.7538402080912.1100836068
82.13278327303-2.036975794891.328167744784.84423554881-1.99022746193.79013570026-0.1777004902960.04616354292360.265738100359-0.142383552637-0.046713664215-0.02748053079470.258182166931-0.3417162827950.1739504259790.1772712527380.009763914053710.03266185114680.300045684912-0.01317711887610.2958572397-8.3103627752121.238914539610.049057608
90.8555594458331.80378423714-0.3385969137726.571320146612.080062690012.88826252631-0.0306189337378-0.1487734464440.4238702572230.2189612623660.9251946603150.0487827085886-0.7030411932550.269387739874-0.62780315360.380112939350.09170170827050.04292262682930.509470705609-0.01509903093940.490652410613-10.217332889740.72349312434.42272605605
101.33023441278-1.151638965880.9102436039133.73380609604-0.5059808190210.641414932757-0.0748412306709-0.0706039078550.7205169823330.950743573314-0.5311483387270.2869271840720.0611378361654-0.575316953450.2142214166390.697923095935-0.1760410511930.243730975530.432894729418-0.1397421934210.848360847228-1.0788671980949.6020633274.86826787116
111.950478691130.683366308588-0.3819767791262.91861461794-2.556880006853.467186539950.1388208977390.1778157547420.1956031745790.16523105110.02937522429370.216651297816-0.311611007299-0.0884206352004-0.1079522245810.2511695659160.0595096367180.03951558241820.2661826735530.001883647124770.270571856971-5.6130734392229.38621872439.63818908573
121.93231616014-0.0010066761677-0.2506345609554.71149816788-0.8728768060282.155679568110.0474175806024-0.06054443250920.3385572663740.282483567780.08540655373560.0989523330956-0.413971300302-0.0613020013313-0.1795961247920.4017356873070.01766331090240.05300189531560.364655004228-0.01750107712290.393578305271-9.7313307649236.426645550315.8846634346
133.078131718760.965473564851-0.8430514189893.74605046206-1.047438004473.69221700069-0.0739222919133-0.02974755232560.06309980562430.3789726722560.114919286103-0.465422290653-0.4690297515990.177733414438-0.09936680155860.3937627234530.008745984314330.006515147030160.305417634994-0.1003907117290.334579135899-1.4185952385937.328483804919.0997585858
142.351902615120.561317396008-2.951390721177.715836064680.3726977392333.80388909843-0.0266560108056-0.012807718615-0.0130434196882-0.06016023195780.04489086182450.307431917020.017758698971-0.647642519105-0.1030539164531.047887577030.170750784325-0.06229305258040.7875672942290.07836418160370.629690726862-12.437266404732.642133442528.0040733073
150.802103642358-0.2867199107570.7955234642261.026599571750.1282131852341.369512421580.206902958807-0.2942031130410.2017999932380.482903805220.4813390875271.19128928628-0.282887759291-0.503667158993-0.6013331548060.4065149538570.08357589543110.1763655735860.3727808229340.1036865622540.562346513537-7.2294578877529.497251468919.0523633866
160.0896323517972-0.621425158758-0.1328734665120.609376443505-0.1206887499371.53375697780.00857575113898-0.06500061611270.07688110709880.04386029642920.0613298170811-0.101662522571-0.1234504789370.166558894084-0.03982027973950.293616460825-0.05288989405680.007214969711330.329300437403-0.007094852581950.3258227721788.6890038358628.55855505087.80693261411
176.44943689532-2.0798595783-0.7007498219475.71339631230.3250071998487.263245823210.0719791217636-0.5517656125320.1094321871670.0879232441425-0.224757607632-0.651161670297-0.3852034260141.13885285344-0.1180380660480.41106931917-0.0840633654430.01612389338480.494950864615-0.002835883444480.4285747374715.505424015827.318175507226.6000026493
182.481191295260.0256020696330.9731827022554.355608791580.00537185049841.324360829290.0227898482212-0.178381266041-0.128638114389-0.03313403119510.166774515985-0.396915718667-0.04390778708420.193314305846-0.1132710850170.282318331505-0.021062032193-0.00513348935220.425144872035-0.02360503812670.2387605727088.5845948723918.507598277925.8454969572
192.437984815640.2797526146990.02865172558261.77491819758-0.5230388749645.50070418545-0.131407310704-0.3564187864220.4117509894680.541599017908-0.002770630841740.130382478193-0.0551122854554-0.124680308490.1546184575620.3896799072770.00754252303016-0.0274690750390.349762200788-0.06000433519280.3184544824152.8633461096627.130543137228.1922239185
201.321603884580.408984216198-0.2769402571681.479427700740.3465392450159.718252743760.110951963433-0.06598509507330.328840711538-0.229666652273-0.173574863438-0.116932067864-0.6659391320971.087774504970.0379415455310.405040630903-0.09402747664760.06049342045810.4157679193960.01655708705170.3767216738787.2467104313638.22231472461.44327002052
211.05926755553-0.4835719132320.09806800798912.54343816222-1.427785178171.372653715090.0802313049379-0.086957226832-0.0224224508108-0.410295866893-0.04390857194770.1015376202420.201276951875-0.0240618589265-0.05685143656950.232841475926-0.008173948742520.0095756127570.3195886414740.01934532521520.3228261334445.3703675759921.5631689362.95594558843
224.950449085450.08449968321741.991216472951.79225744781-0.1354919976693.87062783791-0.02390122297040.225715018876-0.0443103407876-0.203986979949-0.0133634395106-0.2279502420990.297372979601-0.00121354458002-0.03316919035410.1894488716370.002144352562630.02638204440410.2298996706060.006290991188330.2438449213823.5180514502521.2438093728-10.1653992301
230.436513823053-0.8549488249380.8514124689731.73505783869-1.791376548831.783148140280.7748407422160.2595690563950.222671905622-1.408654623060.04383189266421.05871940123-0.427963061634-0.368787644283-0.487253566020.6115023982060.0284558242911-0.02836207142010.377180552220.06490555886690.57807908753-11.452307611529.7979661412-11.3773307781
241.43377730223-2.325752975381.233325048743.88324315036-2.513047857921.943609943280.0432857139069-0.171627714104-0.263278266535-0.2293502965630.123374433430.3938547829420.167377792955-0.15476287934-0.151929022550.235696950928-0.0414981032232-0.00385434367520.328976257954-0.001545705539010.328779244186-1.3556451045415.1918893582-3.60831692954
251.858643046140.246832374067-0.9411960414171.711465555550.4778361503161.56494678443-0.1535130137540.08449670307540.0585676535239-0.3590996051740.1405422794170.01810875685050.170389764661-0.07057194845560.02487277133930.193827382736-0.0134301038611-0.009968519678390.2774532765860.01185204708990.2770985676130.42070866327721.671818775-0.600549659114
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 141 )
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 181 )
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 207 )
5X-RAY DIFFRACTION5chain 'B' and (resid 186 through 190 )
6X-RAY DIFFRACTION6chain 'B' and (resid 191 through 195 )
7X-RAY DIFFRACTION7chain 'B' and (resid 196 through 200 )
8X-RAY DIFFRACTION8chain 'B' and (resid 201 through 210 )
9X-RAY DIFFRACTION9chain 'B' and (resid 211 through 215 )
10X-RAY DIFFRACTION10chain 'B' and (resid 216 through 221 )
11X-RAY DIFFRACTION11chain 'B' and (resid 233 through 248 )
12X-RAY DIFFRACTION12chain 'B' and (resid 249 through 273 )
13X-RAY DIFFRACTION13chain 'B' and (resid 283 through 302 )
14X-RAY DIFFRACTION14chain 'B' and (resid 303 through 308 )
15X-RAY DIFFRACTION15chain 'B' and (resid 314 through 337 )
16X-RAY DIFFRACTION16chain 'B' and (resid 338 through 368 )
17X-RAY DIFFRACTION17chain 'B' and (resid 369 through 378 )
18X-RAY DIFFRACTION18chain 'B' and (resid 379 through 402 )
19X-RAY DIFFRACTION19chain 'B' and (resid 403 through 413 )
20X-RAY DIFFRACTION20chain 'B' and (resid 414 through 423 )
21X-RAY DIFFRACTION21chain 'B' and (resid 424 through 439 )
22X-RAY DIFFRACTION22chain 'B' and (resid 440 through 458 )
23X-RAY DIFFRACTION23chain 'B' and (resid 459 through 471 )
24X-RAY DIFFRACTION24chain 'B' and (resid 472 through 487 )
25X-RAY DIFFRACTION25chain 'B' and (resid 488 through 505 )

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