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- PDB-3kdj: Complex structure of (+)-ABA-bound PYL1 and ABI1 -

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Basic information

Entry
Database: PDB / ID: 3kdj
TitleComplex structure of (+)-ABA-bound PYL1 and ABI1
Components
  • Protein phosphatase 2C 56
  • Putative uncharacterized protein At5g46790
KeywordsHYDROLASE/Hormone Receptor / ABA / PYL1 / ABI1 / Abscisic acid signaling pathway / Cell membrane / Hydrolase / Magnesium / Manganese / Metal-binding / Nucleus / Protein phosphatase / HYDROLASE-Hormone Receptor complex
Function / homology
Function and homology information


regulation of abscisic acid-activated signaling pathway / negative regulation of abscisic acid-activated signaling pathway / protein phosphatase inhibitor complex / regulation of stomatal movement / response to abscisic acid / abscisic acid binding / abscisic acid-activated signaling pathway / plastid / protein phosphatase inhibitor activity / protein-serine/threonine phosphatase ...regulation of abscisic acid-activated signaling pathway / negative regulation of abscisic acid-activated signaling pathway / protein phosphatase inhibitor complex / regulation of stomatal movement / response to abscisic acid / abscisic acid binding / abscisic acid-activated signaling pathway / plastid / protein phosphatase inhibitor activity / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / phosphatase activity / phosphoprotein phosphatase activity / protein dephosphorylation / response to cold / defense response / kinase binding / signaling receptor activity / response to heat / protein kinase binding / protein homodimerization activity / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / 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, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / 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 domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A8S / : / Protein phosphatase 2C 56 / Abscisic acid receptor PYL1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.878 Å
AuthorsYin, P. / Fan, H. / Hao, Q. / Yuan, X. / Yan, N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structural insights into the mechanism of abscisic acid signaling by PYL proteins
Authors: Yin, P. / Fan, H. / Hao, Q. / Yuan, X. / Wu, D. / Pang, Y. / Yan, C. / Li, W. / Wang, J. / Yan, N.
History
DepositionOct 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein At5g46790
B: Protein phosphatase 2C 56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4404
Polymers58,1212
Non-polymers3192
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-16 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.610, 86.788, 110.701
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein At5g46790 / PYL1


Mass: 23327.898 Da / Num. of mol.: 1 / Fragment: residues 20-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g46790 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8VZS8
#2: Protein Protein phosphatase 2C 56 / ABI1 / AtPP2C56 / Protein phosphatase 2C ABI1 / PP2C ABI1 / Protein ABSCISIC ACID-INSENSITIVE 1


Mass: 34792.836 Da / Num. of mol.: 1 / Fragment: residues 119-434 / Mutation: C208S, D378G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ABI1, At4g26080, F20B18.190 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P49597, protein-serine/threonine phosphatase
#3: 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
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M citric acid pH 5.5, 0.01M GSH/GSSG, 10% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.878→34.15 Å / Num. obs: 44478 / % possible obs: 90.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 34.99 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 24.75
Reflection shellResolution: 1.878→1.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 1.87 / Num. unique all: 2581 / % possible all: 53.2

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES: 3KDH and 2P8E

3kdh

2p8e


Resolution: 1.878→34.15 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.718 / SU ML: 0.28 / Isotropic thermal model: TLS / σ(F): 1.34 / Phase error: 33.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 2232 5.03 %Random
Rwork0.2094 42144 --
obs0.2113 44376 90.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.253 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 260.35 Å2 / Biso mean: 60.477 Å2 / Biso min: 30.46 Å2
Baniso -1Baniso -2Baniso -3
1--3.837 Å2-0 Å20 Å2
2---20.564 Å2-0 Å2
3---24.401 Å2
Refinement stepCycle: LAST / Resolution: 1.878→34.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3544 0 20 170 3734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063639
X-RAY DIFFRACTIONf_angle_d1.0444915
X-RAY DIFFRACTIONf_chiral_restr0.069547
X-RAY DIFFRACTIONf_plane_restr0.004642
X-RAY DIFFRACTIONf_dihedral_angle_d15.541352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8784-1.91930.3985600.33021421X-RAY DIFFRACTION48
1.9193-1.96390.35741080.30461767X-RAY DIFFRACTION63
1.9639-2.0130.30631130.2982078X-RAY DIFFRACTION72
2.013-2.06740.31991330.26512332X-RAY DIFFRACTION82
2.0674-2.12820.31951450.2792637X-RAY DIFFRACTION91
2.1282-2.19690.32361360.27112770X-RAY DIFFRACTION96
2.1969-2.27540.32431560.24382834X-RAY DIFFRACTION98
2.2754-2.36650.29031530.23282862X-RAY DIFFRACTION99
2.3665-2.47420.27841420.22692897X-RAY DIFFRACTION99
2.4742-2.60460.26161420.22372877X-RAY DIFFRACTION99
2.6046-2.76770.29981780.22112864X-RAY DIFFRACTION100
2.7677-2.98130.271580.22632889X-RAY DIFFRACTION99
2.9813-3.28110.26151620.22022917X-RAY DIFFRACTION100
3.2811-3.75540.231470.1912957X-RAY DIFFRACTION100
3.7554-4.72940.19251400.16332990X-RAY DIFFRACTION100
4.7294-34.15580.19451590.19183052X-RAY DIFFRACTION98
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)
11.36661.114-0.49772.9315-0.92821.70660.0282-0.03150.05570.246-0.1409-0.4165-0.1360.0770.10180.289-0.0137-0.07990.3102-0.03680.53346.419119.32759.5965
21.91550.57870.80972.11470.76211.39990.1851-0.3117-0.40760.027-0.0005-0.05730.1244-0.2927-0.18020.3685-0.0293-0.0430.3960.08040.562-17.5248-11.46939.3597
30.31480.29960.02020.57030.14840.1114-0.00570.20580.2128-0.091-0.09910.0733-0.1320.16230.0410.5663-0.0182-0.22090.48360.21220.71483.025910.710915.0727
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 31:209A31 - 209
2X-RAY DIFFRACTION2chain B and resid 128:425B128 - 425
3X-RAY DIFFRACTION3chain A and resid 222A222

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