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- PDB-4jdl: Crystal structure of native abscisic acid receptor PYL5 at 2.65 A... -

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Basic information

Entry
Database: PDB / ID: 4jdl
TitleCrystal structure of native abscisic acid receptor PYL5 at 2.65 Angstrom
ComponentsAbscisic acid receptor PYL5
KeywordsHORMONE RECEPTOR / abscisic acid receptor / PP2C
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / nucleus / plasma membrane / cytoplasm
Similarity search - Function
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
Abscisic acid receptor PYL5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsZhang, X. / Zhang, Q. / Chen, Z.
CitationJournal: Plos One / Year: 2013
Title: Structural Insights into the Abscisic Acid Stereospecificity by the ABA Receptors PYR/PYL/RCAR
Authors: Zhang, X. / Jiang, L. / Wang, G. / Yu, L. / Zhang, Q. / Xin, Q. / Wu, W. / Gong, Z. / Chen, Z.
History
DepositionFeb 25, 2013Deposition site: RCSB / Processing site: PDBJ
SupersessionMar 13, 2013ID: 3QRZ
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

Downloads & links

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Assembly

Deposited unit
A: Abscisic acid receptor PYL5
B: Abscisic acid receptor PYL5
C: Abscisic acid receptor PYL5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,00915
Polymers74,9043
Non-polymers1,10512
Water10,178565
1
A: Abscisic acid receptor PYL5
C: Abscisic acid receptor PYL5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,67310
Polymers49,9362
Non-polymers7378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Abscisic acid receptor PYL5
hetero molecules

B: Abscisic acid receptor PYL5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,67310
Polymers49,9362
Non-polymers7378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
Unit cell
Length a, b, c (Å)95.850, 95.850, 143.968
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-423-

HOH

21C-560-

HOH

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Components

#1: Protein Abscisic acid receptor PYL5 / ABI1-binding protein 3 / PYR1-like protein 5 / Regulatory components of ABA receptor 8


Mass: 24967.951 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL5 / Plasmid: pet-28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) cells / References: UniProt: Q9FLB1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 13% peg3k, 0.1M tris, 5% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97877 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97877 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.5
11K, H, -L20.5
ReflectionResolution: 2.55→50 Å / Num. all: 24503 / Num. obs: 23999 / % possible obs: 98 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.55→2.59 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
BALBESphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3KLX

3klx


Resolution: 2.65→47.92 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.888 / SU B: 7.479 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27444 1082 5.1 %RANDOM
Rwork0.25349 ---
all0.25462 20500 --
obs0.25462 20210 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.353 Å2
Baniso -1Baniso -2Baniso -3
1--20.53 Å2-0 Å2-0 Å2
2---20.53 Å2-0 Å2
3---41.06 Å2
Refinement stepCycle: LAST / Resolution: 2.65→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3200 0 72 565 3837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193316
X-RAY DIFFRACTIONr_bond_other_d0.0020.022995
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9554482
X-RAY DIFFRACTIONr_angle_other_deg0.86736852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2525420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97422.256133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.07315474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3341531
X-RAY DIFFRACTIONr_chiral_restr0.0730.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213691
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02749
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.48 78 -
Rwork0.326 1510 -
obs--99.87 %

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