[English] 日本語
Yorodumi
- PDB-3neg: Pyrabactin-bound PYL1 structure in the open and close forms -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3neg
TitlePyrabactin-bound PYL1 structure in the open and close forms
ComponentsAbscisic acid receptor PYL1
KeywordsHYDROLASE / PYL1 / pyrabactin / HORMONE RECEPTOR
Function / homology
Function and homology information


protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / plastid / protein phosphatase inhibitor activity / defense response / signaling receptor activity / protein homodimerization activity / identical protein binding / nucleus ...protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / plastid / protein phosphatase inhibitor activity / defense response / 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
BROMIDE ION / Chem-PYV / Abscisic acid receptor PYL1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsYan, N.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Functional mechanism of the ABA agonist pyrabactin
Authors: Hao, Q. / Yin, P. / Yan, C. / Yuan, X. / Li, W. / Zhang, Z. / Liu, L. / Wang, J. / Yan, N.
History
DepositionJun 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Abscisic acid receptor PYL1
B: Abscisic acid receptor PYL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4905
Polymers46,6562
Non-polymers8343
Water362
1
A: Abscisic acid receptor PYL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7853
Polymers23,3281
Non-polymers4572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Abscisic acid receptor PYL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7052
Polymers23,3281
Non-polymers3771
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.23, 130.23, 88.25
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Abscisic acid receptor PYL1 / PYL1 / PYR1-like protein 1 / ABI1-binding protein 6 / Regulatory components of ABA receptor 9


Mass: 23327.898 Da / Num. of mol.: 2 / Fragment: UNP residues 20-221
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: Q8VZS8, protein-serine/threonine phosphatase
#2: Chemical ChemComp-PYV / 4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide / Pyrabactin


Mass: 377.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13BrN2O2S
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.63 Å3/Da / Density % sol: 73.44 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M citric acid pH 5.5, 0.01M GSH/GSSG, 10% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.92001 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92001 Å / Relative weight: 1
ReflectionResolution: 2.801→69.503 Å / Num. obs: 38331 / % possible obs: 93.1 % / Redundancy: 6 % / Biso Wilson estimate: 61.52 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.5
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 3.4 / % possible all: 54.5

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KDJ

3kdj


Resolution: 2.801→69.503 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.833 / SU ML: 0.4 / σ(F): 1.3 / Phase error: 23.93 / Stereochemistry target values: ML / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING.
RfactorNum. reflection% reflection
Rfree0.2423 1955 5.1 %
Rwork0.1951 36376 -
obs0.1974 38331 93.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.266 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 224.92 Å2 / Biso mean: 86.227 Å2 / Biso min: 36.09 Å2
Baniso -1Baniso -2Baniso -3
1-13.0045 Å2-0 Å2-0 Å2
2--13.0045 Å20 Å2
3----26.0091 Å2
Refinement stepCycle: LAST / Resolution: 2.801→69.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2870 0 45 2 2917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092967
X-RAY DIFFRACTIONf_angle_d1.1984022
X-RAY DIFFRACTIONf_dihedral_angle_d18.9181080
X-RAY DIFFRACTIONf_chiral_restr0.071454
X-RAY DIFFRACTIONf_plane_restr0.004522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8013-2.87130.313420.2571284X-RAY DIFFRACTION45
2.8713-2.9490.2721240.26381741X-RAY DIFFRACTION63
2.949-3.03580.28861510.27572658X-RAY DIFFRACTION96
3.0358-3.13370.29731480.26572790X-RAY DIFFRACTION100
3.1337-3.24570.28551470.23442771X-RAY DIFFRACTION100
3.2457-3.37570.24431490.22212788X-RAY DIFFRACTION100
3.3757-3.52930.23091520.19222806X-RAY DIFFRACTION100
3.5293-3.71540.23011510.18552795X-RAY DIFFRACTION100
3.7154-3.94810.19961270.16332816X-RAY DIFFRACTION100
3.9481-4.25290.18831500.15082780X-RAY DIFFRACTION100
4.2529-4.68090.19331580.14482780X-RAY DIFFRACTION100
4.6809-5.3580.21081480.15852796X-RAY DIFFRACTION100
5.358-6.74960.24421800.17452762X-RAY DIFFRACTION100
6.7496-69.52420.23461280.18742809X-RAY DIFFRACTION99
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)
12.75950.1142-0.16912.20741.45794.8094-0.1847-0.07920.0867-0.01260.07610.0181-0.09860.2493-0.00020.3486-0.0685-0.03060.3101-0.03440.3432-56.552137.313-12.3824
21.88391.3233-0.58131.716-0.18314.24090.0369-0.0145-0.16620.00030.269-0.0514-0.4160.6103-0.00030.4208-0.399-0.07180.7060.0130.5154-43.497756.73063.2108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA3 - 189
2X-RAY DIFFRACTION2chain BB9 - 191

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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