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- PDB-3jrs: Crystal structure of (+)-ABA-bound PYL1 -

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Basic information

Entry
Database: PDB / ID: 3jrs
TitleCrystal structure of (+)-ABA-bound PYL1
ComponentsPutative uncharacterized protein At5g46790
KeywordsHormone Receptor / Plant Hormone Receptor / Abscisic acid / PYL1
Function / homologyPolyketide cyclase/dehydrase / START-like domain superfamily / Polyketide cyclase / dehydrase and lipid transport / abscisic acid binding / regulation of protein serine/threonine phosphatase activity / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / protein homodimerization activity / identical protein binding ...Polyketide cyclase/dehydrase / START-like domain superfamily / Polyketide cyclase / dehydrase and lipid transport / abscisic acid binding / regulation of protein serine/threonine phosphatase activity / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / protein homodimerization activity / identical protein binding / plasma membrane / nucleus / cytoplasm / Abscisic acid receptor PYL1
Function and homology information
Specimen sourceArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 2.05 Å resolution
AuthorsMiyazono, K. / Miyakawa, T. / Sawano, Y. / Kubota, K. / Tanokura, M.
CitationJournal: Nature / Year: 2009
Title: Structural basis of abscisic acid signalling
Authors: Miyazono, K. / Miyakawa, T. / Sawano, Y. / Kubota, K. / Kang, H.J. / Asano, A. / Miyauchi, Y. / Takahashi, M. / Zhi, Y. / Fujita, Y. / Yoshida, T. / Kodaira, K. / Yamaguchi-Shinozaki, K. / Tanokura, M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 8, 2009 / Release: Nov 3, 2009
RevisionDateData content typeGroupProviderType
1.0Nov 3, 2009Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelAdvisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein At5g46790
B: Putative uncharacterized protein At5g46790
C: Putative uncharacterized protein At5g46790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7056
Polyers71,9123
Non-polymers7933
Water5,657314
1
A: Putative uncharacterized protein At5g46790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2352
Polyers23,9711
Non-polymers2641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein At5g46790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2352
Polyers23,9711
Non-polymers2641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative uncharacterized protein At5g46790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2352
Polyers23,9711
Non-polymers2641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)97.730, 97.730, 135.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP 41 21 2

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Components

#1: Protein/peptide Putative uncharacterized protein At5g46790 / PYL1


Mass: 23970.598 Da / Num. of mol.: 3 / Fragment: UNP residues 8-211 / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid name: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VZS8
#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.: 3 / Formula: C15H20O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.25 / Density percent sol: 45.23 %
Crystal growTemp: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M HEPES, pH 8.0, 24% PEG3350, 0.2 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperatureCrystal ID
1951
2951
Source
SourceSiteBeamlineIdWavelength
SYNCHROTRONPhoton Factory BL-5A11.0000
SYNCHROTRONPhoton Factory BL-5A20.97926, 0.97942, 0.96418
Detector
TypeIdDetector
ADSC QUANTUM 315r1CCD
ADSC QUANTUM 315r2CCD
Radiation
IdDiffraction protocolMonochromatic or laue m lScattering typeWavelength ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelengthRelative weight
11.00001.0
20.979261.0
30.979421.0
40.964181.0
ReflectionB iso Wilson estimate: 39.378 Å2 / D resolution high: 2.05 Å / D resolution low: 20 Å / Number obs: 41716 / Observed criterion sigma I: -3 / Rmerge I obs: 0.057 / NetI over sigmaI: 32.29 / Percent possible obs: 99.8
Reflection shell

Diffraction ID: 1,2

Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsNumber measured obsNumber unique obsPercent possible all
0.5162.052.106.2441133031100.00
0.4642.102.166.9432822975100.00
0.3552.162.228.9419282889100.00
0.2722.222.2911.4404912784100.00
0.2332.292.3713.0393462708100.00
0.1912.372.4515.3385322658100.00
0.1602.452.5418.3369442543100.00
0.1262.542.6522.1356842464100.00
0.0982.652.7627.1341032358100.00
0.0812.762.9032.3323292240100.00
0.0652.903.0638.2311762166100.00
0.0523.063.2447.1291992040100.00
0.0413.243.4756.6275311936100.00
0.0373.473.7462.7253861795100.00
0.0323.744.1071.1234271680100.00
0.0314.104.5875.1208311517100.00
0.0314.585.2975.9181291355100.00
0.0305.296.4874.7156231168100.00
0.0256.489.1779.91242492999.90
0.0219.172079.6575248085.70

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Processing

Software
NameVersionClassificationContact authorLocationTypeContact author emailDateLanguage
XSCALEdata scalingWolfgang Kabschhttp://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.htmlpackage
REFMACrefmac_5.5.0088refinementGarib N. Murshudovhttp://www.ccp4.ac.uk/dist/html/refmac5.htmlprogramgarib[at]ysbl.york.ac.uk24/04/2001Fortran_77
PDB_EXTRACT3.005data extractionPDBhttp://sw-tools.pdb.org/apps/PDB_EXTRACT/packagehelp[at]deposit.rcsb.orgJune 11, 2008C++
XDSdata reduction
RefineMethod to determine structure: MAD / Correlation coeff Fo to Fc: 0.953 / Correlation coeff Fo to Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.5 / Overall SU B: 9.009 / Overall SU ML: 0.111 / R Free selection details: RANDOM / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R: 0.18 / Overall ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.4 Å / Solvent model details: MASK
Displacement parametersB iso max: 55.47 Å2 / B iso mean: 24.221 Å2 / B iso min: 8.61 Å2 / Aniso B11: 0.06 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 0.06 Å2 / Aniso B23: 0 Å2 / Aniso B33: -0.11 Å2
Least-squares processR factor R free: 0.229 / R factor R work: 0.19 / R factor obs: 0.192 / Highest resolution: 2.05 Å / Lowest resolution: 2 Å / Number reflection R free: 2109 / Number reflection obs: 41713 / Percent reflection R free: 5.1 / Percent reflection obs: 99.96
Refine hist #LASTHighest resolution: 2.05 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 4104 / Nucleic acid: 0 / Ligand: 57 / Solvent: 314 / Total: 4475
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0214230
X-RAY DIFFRACTIONr_angle_refined_deg2.3131.9565732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4015.000499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.63922.909220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68715.000728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.27915.00050
X-RAY DIFFRACTIONr_chiral_restr0.1750.200654
X-RAY DIFFRACTIONr_gen_planes_refined0.0100.0213217
X-RAY DIFFRACTIONr_mcbond_it1.1961.5002521
X-RAY DIFFRACTIONr_mcangle_it2.0672.0004109
X-RAY DIFFRACTIONr_scbond_it3.3353.0001709
X-RAY DIFFRACTIONr_scangle_it5.0004.5001623
Refine LS shellHighest resolution: 2.05 Å / R factor R free: 0.285 / R factor R work: 0.211 / Lowest resolution: 2.103 Å / Number reflection R free: 140 / Number reflection R work: 2856 / Number reflection all: 2996 / Total number of bins used: 20 / Percent reflection obs: 1
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
12.09300.1894-0.93822.74070.42752.84850.0379-0.16240.0640-0.08910.16240.0477-0.10670.3846-0.20020.0298-0.03210.03900.0706-0.03520.083029.3470-11.775027.3880
21.5766-0.09910.16092.30511.67543.69460.1310-0.0851-0.0522-0.1127-0.13250.0775-0.0320-0.09190.00140.0239-0.01490.00180.0445-0.00680.051159.6670-4.573031.5630
33.0507-0.79930.21272.12840.24341.54520.32970.31990.0026-0.3670-0.3695-0.1281-0.08640.03740.03980.09250.08960.01430.09880.02270.025583.2760-16.787017.4830
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS ID
1A31A2091
2A1A11
3B30B2092
4B2B22
5C38C2093
6C3C33

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