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- PDB-3kl1: Crystal structure of abscisic acid receptor PYL2 at 1.55 A -

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Basic information

Entry
Database: PDB / ID: 3kl1
TitleCrystal structure of abscisic acid receptor PYL2 at 1.55 A
ComponentsPutative uncharacterized protein At2g26040
KeywordsHORMONE RECEPTOR / abscisic acid receptor / crystal / high resolution / PP2C
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 / MAD / Resolution: 1.55 Å
AuthorsZhang, X. / Wang, G. / Chen, Z.
CitationJournal: Structure / Year: 2012
Title: Complex Structures of the Abscisic Acid Receptor PYL3/RCAR13 Reveal a Unique Regulatory Mechanism
Authors: Zhang, X. / Zhang, Q. / Xin, Q. / Yu, L. / Wang, Z. / Wu, W. / Jiang, L. / Wang, G. / Tian, W. / Deng, Z. / Wang, Y. / Liu, Z. / Long, J. / Gong, Z. / Chen, Z.
History
DepositionNov 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 6, 2012Group: Database references
Revision 1.3Mar 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


Theoretical massNumber of molelcules
Total (without water)42,6202
Polymers42,6202
Non-polymers00
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-13 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.143, 61.143, 184.769
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Putative uncharacterized protein At2g26040 / PYL2


Mass: 21309.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g26040, PYL2 / Plasmid: pgex 4t-2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: O80992
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8
Details: 20mM tris, 30% Peg4k, pH 8.0, EVAPORATION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11301
21301
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NE3A10.97943, 0.97960, 0.96438
SYNCHROTRONPhoton Factory AR-NW12A21.9
Detector
TypeIDDetectorDate
ADSC QUANTUM 2701CCDOct 25, 2009
ADSC QUANTUM 2702CCDOct 25, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979431
20.97961
30.964381
41.91
ReflectionResolution: 1.55→50 Å / Num. all: 59264 / Num. obs: 57490 / % possible obs: 97 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 10.6 % / Rsym value: 0.047 / Net I/σ(I): 0.056
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.654 / % possible all: 5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.55→50 Å / σ(F): 3 / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 2719 -random
Rwork0.2013 ---
all0.2024 59264 --
obs0.2024 57490 97 %-
Refinement stepCycle: LAST / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 0 241 3020
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d1.49362
X-RAY DIFFRACTIONc_bond_d0.00719

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