[English] 日本語
Yorodumi
- PDB-3jrq: Crystal structure of (+)-ABA-bound PYL1 in complex with ABI1 -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 3jrq
TitleCrystal structure of (+)-ABA-bound PYL1 in complex with ABI1
Components
  • Protein phosphatase 2C 56
  • Putative uncharacterized protein At5g46790
KeywordsHYDROLASE/Hormone Receptor / Plant Hormone Receptor / Abscisic acid / PYL1 / ABI1 / type 2C protein phosphatase / Abscisic acid signaling pathway / Cell membrane / Hydrolase / Magnesium / Manganese / Membrane / Metal-binding / Nucleus / Protein phosphatase / HYDROLASE-Hormone Receptor COMPLEX
Function / homologyPPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain / Protein phosphatase 2C family / Polyketide cyclase/dehydrase / PPM-type phosphatase domain profile. / PPM-type phosphatase domain signature. / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C / START-like domain superfamily / PPM-type phosphatase domain superfamily ...PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain / Protein phosphatase 2C family / Polyketide cyclase/dehydrase / PPM-type phosphatase domain profile. / PPM-type phosphatase domain signature. / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C / START-like domain superfamily / PPM-type phosphatase domain superfamily / regulation of abscisic acid-activated signaling pathway / negative regulation of abscisic acid-activated signaling pathway / regulation of stomatal movement / response to abscisic acid / magnesium-dependent protein serine/threonine phosphatase activity / abscisic acid binding / regulation of protein serine/threonine phosphatase activity / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / phosphatase activity / phosphoprotein phosphatase activity / response to cold / protein dephosphorylation / kinase binding / response to heat / signaling receptor activity / protein kinase binding / protein homodimerization activity / identical protein binding / plasma membrane / nucleus / metal ion binding / cytosol / cytoplasm / Protein phosphatase 2C 56 / Abscisic acid receptor PYL1
Function and homology information
Specimen sourceArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.1 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein phosphatase 2C 56
B: Putative uncharacterized protein At5g46790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5873
Polyers57,3232
Non-polymers2641
Water1,928107
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)1730
ΔGint (kcal/M)-10
Surface area (Å2)19640
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)49.010, 60.620, 84.960
Angle α, β, γ (deg.)90.00, 104.56, 90.00
Int Tables number4
Space group name H-MP 1 21 1

-
Components

#1: Protein/peptide Protein phosphatase 2C 56 / AtPP2C56 / Protein phosphatase 2C ABI1 / PP2C ABI1 / Protein ABSCISIC ACID-INSENSITIVE 1


Mass: 35875.992 Da / Num. of mol.: 1 / Fragment: UNP residues 125-429 / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ABI1 / Plasmid name: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: P49597, protein-serine/threonine phosphatase
#2: Protein/peptide Putative uncharacterized protein At5g46790 / PYL1


Mass: 21446.926 Da / Num. of mol.: 1 / Fragment: UNP residues 28-210 / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid name: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VZS8
#3: 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 / Formula: C15H20O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Formula: H2O / Water

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.13 / Density percent sol: 42.28 %
Crystal growTemp: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 21% PEG3000, 0.1 M sodium citrate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 95 kelvins
SourceSource: SYNCHROTRON / Type: PHOTON FACTORY BEAMLINE AR-NW12A / Synchrotron site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1
DetectorType: ADSC QUANTUM 210r / Detector: CCD
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 45.868 Å2 / D resolution high: 2.1 Å / D resolution low: 20 Å / Number obs: 26472 / Observed criterion sigma I: -3 / Rmerge I obs: 0.093 / NetI over sigmaI: 10.88 / Percent possible obs: 93.3
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsNumber measured obsNumber unique obsPercent possible all
0.3482.102.152.44264162178.10
0.2902.152.212.94543170883.30
0.2642.212.283.24530165784.90
0.3602.282.353.76256173788.90
0.3172.352.424.77904173293.40
0.3152.422.515.58865171495.90
0.2802.512.606.29090165494.80
0.2372.602.717.69123161296.30
0.1992.712.838.98853155597.80
0.1652.832.9710.98703149296.90
0.1362.973.1313.28503143997.40
0.1193.133.3216.28133136098.60
0.0993.323.5519.07840130699.20
0.0973.553.8320.67315120799.40
0.0873.834.2021.96753110498.70
0.0704.204.7023.66341102099.40
0.0694.705.4223.5566190399.80
0.0795.426.6422.6485776599.20
0.0626.649.3923.2370159699.30
0.0509.392021.3159729082.60

-
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: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A6Q and 3JRS
Correlation coeff Fo to Fc: 0.956 / Correlation coeff Fo to Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 1 / Overall SU B: 12.402 / Overall SU ML: 0.148 / R Free selection details: RANDOM / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R: 0.252 / Overall ESU R Free: 0.206 / 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: 58.84 Å2 / B iso mean: 30.132 Å2 / B iso min: 8.86 Å2 / Aniso B11: 0.03 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0.03 Å2 / Aniso B22: 0.03 Å2 / Aniso B23: 0 Å2 / Aniso B33: -0.04 Å2
Least-squares processR factor R free: 0.249 / R factor R work: 0.198 / R factor obs: 0.201 / Highest resolution: 2.1 Å / Lowest resolution: 2 Å / Number reflection R free: 1326 / Number reflection obs: 26467 / Percent reflection R free: 5 / Percent reflection obs: 93.38
Refine hist #LASTHighest resolution: 2.1 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 3493 / Nucleic acid: 0 / Ligand: 19 / Solvent: 107 / Total: 3619
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223576
X-RAY DIFFRACTIONr_angle_refined_deg2.1691.9594838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3835.000439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.35423.095168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.75515.000617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.72215.00036
X-RAY DIFFRACTIONr_chiral_restr0.1600.200543
X-RAY DIFFRACTIONr_gen_planes_refined0.0100.0212704
X-RAY DIFFRACTIONr_mcbond_it1.1751.5002207
X-RAY DIFFRACTIONr_mcangle_it2.0992.0003565
X-RAY DIFFRACTIONr_scbond_it3.4253.0001369
X-RAY DIFFRACTIONr_scangle_it5.3404.5001273
Refine LS shellHighest resolution: 2.1 Å / R factor R free: 0.338 / R factor R work: 0.293 / Lowest resolution: 2.155 Å / Number reflection R free: 80 / Number reflection R work: 1541 / Number reflection all: 1621 / Total number of bins used: 20 / Percent reflection obs: 78.2
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
11.3100-0.2158-0.28823.37561.71743.13480.0150-0.03020.09470.04000.0108-0.2085-0.20910.1064-0.02580.0879-0.0460-0.00610.08090.00520.0227-5.2265-8.555328.9410
21.61040.28760.30301.20720.45081.66560.00690.00090.0042-0.04540.02500.0252-0.00310.1241-0.03190.00760.00340.00080.0821-0.01840.1125-13.9624-30.3365-1.0708
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS ID
1A125A4231
2B32B2102
3B1B12

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at EBI / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more