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- PDB-3kdh: Structure of ligand-free PYL2 -

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Basic information

Entry
Database: PDB / ID: 3kdh
TitleStructure of ligand-free PYL2
ComponentsPutative uncharacterized protein At2g26040
KeywordsHORMONE RECEPTOR / PYL2
Function / homology
Function and homology information


protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / protein homodimerization activity / identical protein binding / 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 PYL2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.653 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 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein At2g26040
B: Putative uncharacterized protein At2g26040
C: Putative uncharacterized protein At2g26040


Theoretical massNumber of molelcules
Total (without water)63,9303
Polymers63,9303
Non-polymers00
Water18,4111022
1
A: Putative uncharacterized protein At2g26040
B: Putative uncharacterized protein At2g26040


Theoretical massNumber of molelcules
Total (without water)42,6202
Polymers42,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-14 kcal/mol
Surface area19240 Å2
MethodPISA
2
C: Putative uncharacterized protein At2g26040

C: Putative uncharacterized protein At2g26040


Theoretical massNumber of molelcules
Total (without water)42,6202
Polymers42,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_355-x-2,y,-z+1/21
Buried area1700 Å2
ΔGint-12 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.486, 105.483, 187.912
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-239-

HOH

21C-244-

HOH

31C-488-

HOH

41C-939-

HOH

51C-971-

HOH

61C-995-

HOH

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Components

#1: Protein Putative uncharacterized protein At2g26040 / PYL2


Mass: 21309.938 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O80992
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1022 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1M sodium citrate tribasic, 100mM Tris, pH8.5, 79mM MEGA-8 (Octanoyl-N-methylglucamide), 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: Jul 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.653→30.82 Å / Num. obs: 73929 / % possible obs: 98.6 % / Redundancy: 4 % / Biso Wilson estimate: 17.79 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 32.76
Reflection shellResolution: 1.653→1.71 Å / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 6.54 / % possible all: 94.4

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.653→30.82 Å / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.876 / SU ML: 0.2 / Isotropic thermal model: TLS / σ(F): 0.05 / Phase error: 19.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 3480 4.82 %Thin Shell
Rwork0.1746 68735 --
obs0.1762 72215 96.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.664 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 107.6 Å2 / Biso mean: 26.027 Å2 / Biso min: 5.59 Å2
Baniso -1Baniso -2Baniso -3
1--3.279 Å20 Å20 Å2
2--0.541 Å2-0 Å2
3---2.739 Å2
Refinement stepCycle: LAST / Resolution: 1.653→30.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4589 0 0 1022 5611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064725
X-RAY DIFFRACTIONf_angle_d1.036477
X-RAY DIFFRACTIONf_chiral_restr0.073759
X-RAY DIFFRACTIONf_plane_restr0.004845
X-RAY DIFFRACTIONf_dihedral_angle_d14.4451815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6527-1.6754000.1842702X-RAY DIFFRACTION94
1.6754-1.69930.22132870.17912518X-RAY DIFFRACTION95
1.6993-1.7247000.1712773X-RAY DIFFRACTION95
1.7247-1.75160.21752640.17272590X-RAY DIFFRACTION95
1.7516-1.7803000.17922797X-RAY DIFFRACTION96
1.7803-1.8110.2252800.18422579X-RAY DIFFRACTION96
1.811-1.844000.17772844X-RAY DIFFRACTION96
1.844-1.87940.22082540.16892589X-RAY DIFFRACTION96
1.8794-1.9178000.16982854X-RAY DIFFRACTION95
1.9178-1.95950.19342480.16022547X-RAY DIFFRACTION96
1.9595-2.0050.19932190.16052650X-RAY DIFFRACTION98
2.005-2.0552000.16342937X-RAY DIFFRACTION99
2.0552-2.11070.20112170.16712730X-RAY DIFFRACTION99
2.1107-2.1728000.16692925X-RAY DIFFRACTION99
2.1728-2.24290.22372160.16792654X-RAY DIFFRACTION96
2.2429-2.32310.21272180.17492610X-RAY DIFFRACTION95
2.3231-2.416000.17262943X-RAY DIFFRACTION99
2.416-2.5260.22362150.1772741X-RAY DIFFRACTION99
2.526-2.65910.22491740.1842805X-RAY DIFFRACTION99
2.6591-2.82560.21091910.18232807X-RAY DIFFRACTION100
2.8256-3.04350.18521680.17872802X-RAY DIFFRACTION99
3.0435-3.34950.17321530.1662825X-RAY DIFFRACTION99
3.3495-3.83340.19641280.15922814X-RAY DIFFRACTION97
3.8334-4.82670.16841170.14712848X-RAY DIFFRACTION97
4.8267-30.82530.22721310.19092851X-RAY DIFFRACTION94
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)
10.81990.0181-0.31011.06880.20620.8050.0650.04840.1098-0.04090.00330.0793-0.0148-0.0458-0.06210.0744-0.00080.02170.01310.00160.0106-31.3854-1.710321.142
21.2573-0.0603-0.09840.90890.17070.68380.0207-0.0229-0.09070.05950.0403-0.0422-0.03150.0492-0.05760.07640.0063-0.01640.0808-0.01780.0465-18.8938-25.10549.9533
30.96740.3655-0.06061.06370.40370.81140.0329-0.0791-0.04530.0980.046-0.18090.03470.0036-0.08080.1307-0.02110.00590.0927-0.02620.0775-49.3027-26.691641.19
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and not waterA0
2X-RAY DIFFRACTION2chain B and not waterB0
3X-RAY DIFFRACTION3chain C and not waterC0

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