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- PDB-3k3k: Crystal structure of dimeric abscisic acid (ABA) receptor pyrabac... -

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Basic information

Entry
Database: PDB / ID: 3k3k
TitleCrystal structure of dimeric abscisic acid (ABA) receptor pyrabactin resistance 1 (PYR1) with ABA-bound closed-lid and ABA-free open-lid subunits
ComponentsAbscisic acid receptor PYR1
KeywordsHORMONE RECEPTOR / SIGNALING PROTEIN / PYR1 / ABSCISIC ACID / ABA RECEPTOR / PLANT HORMONE RECEPTOR / ABA / ABA SENSOR / DROUGHT TOLERANCE / PLANT DEVELOPMENT / SEED DORMANCY / ALPHA/BETA HELIX-GRIP FOLD / START PROTEIN / CLUSTER A TYPE 2C PROTEIN PHOSPHATASE (PP2C) INHIBITOR / PYRABACTIN RESISTANCE 1 / PYRABACTIN / PYL / PHYTOHORMONE
Function / homology
Function and homology information


positive regulation of response to water deprivation / regulation of protein serine/threonine phosphatase activity / plant-type vacuole membrane / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / ubiquitin-like protein ligase binding / signaling receptor activity / protein homodimerization activity ...positive regulation of response to water deprivation / regulation of protein serine/threonine phosphatase activity / plant-type vacuole membrane / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / ubiquitin-like protein ligase binding / signaling receptor activity / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Polyketide cyclase / dehydrase and lipid transport / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A8S / Abscisic acid receptor PYR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsArvai, A.S. / Hitomi, K. / Getzoff, E.D.
CitationJournal: Science / Year: 2009
Title: Structural mechanism of abscisic acid binding and signaling by dimeric PYR1.
Authors: Nishimura, N. / Hitomi, K. / Arvai, A.S. / Rambo, R.P. / Hitomi, C. / Cutler, S.R. / Schroeder, J.I. / Getzoff, E.D.
History
DepositionOct 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Abscisic acid receptor PYR1
B: Abscisic acid receptor PYR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8143
Polymers47,5492
Non-polymers2641
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-14 kcal/mol
Surface area19430 Å2
MethodPISA
2
A: Abscisic acid receptor PYR1
B: Abscisic acid receptor PYR1
hetero molecules

A: Abscisic acid receptor PYR1
B: Abscisic acid receptor PYR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6276
Polymers95,0984
Non-polymers5292
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6320 Å2
ΔGint-33.9 kcal/mol
Surface area35570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.208, 61.407, 82.844
Angle α, β, γ (deg.)90.000, 98.970, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-216-

HOH

21A-314-

HOH

31A-327-

HOH

41A-333-

HOH

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Components

#1: Protein Abscisic acid receptor PYR1 / PYRABACTIN RESISTANCE 1 / GENE PRODUCT AT4G17870 / REGULATORY COMPONENT OF ABA RECEPTOR 11 / RCAR11 ...PYRABACTIN RESISTANCE 1 / GENE PRODUCT AT4G17870 / REGULATORY COMPONENT OF ABA RECEPTOR 11 / RCAR11 / GENE PRODUCT T6K21.50


Mass: 23774.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT4g17870, PYR1, T6K21.50 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O49686
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.2
Details: 20% PEG MME 2000, 5% Ammonium sulfate, 5% NaCl, pH 6.2, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.115932 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115932 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 53191 / Num. obs: 53191 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 22.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4195 / Rsym value: 0.391 / % possible all: 76.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F08

3f08


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.644 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.101 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2685 5.1 %RANDOM
Rwork0.189 ---
all0.191 53122 --
obs0.191 53122 96.72 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 0.9 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 316.53 Å2 / Biso mean: 53.873 Å2 / Biso min: 9.71 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å20 Å21.3 Å2
2---2.57 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 19 380 3323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223134
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.9554271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1085400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.36323.333156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99515564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6651532
X-RAY DIFFRACTIONr_chiral_restr0.1140.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022406
X-RAY DIFFRACTIONr_nbd_refined0.2140.21469
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22154
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2304
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.230
X-RAY DIFFRACTIONr_mcbond_it16.8641.51954
X-RAY DIFFRACTIONr_mcangle_it19.83523112
X-RAY DIFFRACTIONr_scbond_it40.10131314
X-RAY DIFFRACTIONr_scangle_it42.3474.51143
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 172 -
Rwork0.301 2873 -
all-3045 -
obs--75.43 %

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