[English] 日本語
Yorodumi
- PDB-3nr4: Pyrabactin-bound PYL2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nr4
TitlePyrabactin-bound PYL2
ComponentsAbscisic acid receptor PYL2
KeywordsHORMONE RECEPTOR / Abscisic acid signaling pathway / Receptor / Pyrabactin
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
Chem-PYV / Abscisic acid receptor PYL2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 Å
AuthorsYan, N.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Single amino acid alteration between Valine and Isoleucine determines the distinct pyrabactin selectivity by PYL1 and PYL2
Authors: Yuan, X. / Yin, P. / Hao, Q. / Yan, C. / Wang, J. / Yan, N.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 14, 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 PYL2
B: Abscisic acid receptor PYL2
C: Abscisic acid receptor PYL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0626
Polymers63,9303
Non-polymers1,1323
Water6,179343
1
A: Abscisic acid receptor PYL2
B: Abscisic acid receptor PYL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3744
Polymers42,6202
Non-polymers7552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-16 kcal/mol
Surface area18260 Å2
MethodPISA
2
C: Abscisic acid receptor PYL2
hetero molecules

C: Abscisic acid receptor PYL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3744
Polymers42,6202
Non-polymers7552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area1710 Å2
ΔGint-17 kcal/mol
Surface area17600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.950, 106.120, 187.990
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-249-

HOH

-
Components

#1: Protein Abscisic acid receptor PYL2 / PYL2 / PYR1-like protein 2 / Regulatory components of ABA receptor 14


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: Chemical ChemComp-PYV / 4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide / Pyrabactin


Mass: 377.256 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H13BrN2O2S / Comment: hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.90635 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2010
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90635 Å / Relative weight: 1
ReflectionResolution: 2.006→46.998 Å / Num. obs: 81451 / % possible obs: 92 % / Observed criterion σ(I): 1.93 / Redundancy: 2.1 % / Biso Wilson estimate: 28.86 Å2 / Rmerge(I) obs: 0.083
Reflection shellResolution: 2.006→2.13 Å / Rmerge(I) obs: 44.9 / Num. unique all: 11920 / % possible all: 90.4

-
Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KDH

3kdh


Resolution: 2.006→46.998 Å / Occupancy max: 1 / Occupancy min: 0.69 / FOM work R set: 0.8344 / SU ML: 0.3 / σ(F): 1.01 / Phase error: 24.12 / Stereochemistry target values: ML / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING.
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 3621 4.9 %Thin Shell
Rwork0.1894 70215 --
obs0.1918 73836 90.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.251 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso max: 146.78 Å2 / Biso mean: 36.8357 Å2 / Biso min: 12.19 Å2
Baniso -1Baniso -2Baniso -3
1--2.1135 Å20 Å20 Å2
2--0.2872 Å2-0 Å2
3---1.8264 Å2
Refinement stepCycle: LAST / Resolution: 2.006→46.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4131 0 66 343 4540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084281
X-RAY DIFFRACTIONf_angle_d1.0335824
X-RAY DIFFRACTIONf_dihedral_angle_d15.9111540
X-RAY DIFFRACTIONf_chiral_restr0.073686
X-RAY DIFFRACTIONf_plane_restr0.004738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0064-2.0328000.27622509X-RAY DIFFRACTION81
2.0328-2.0607000.27762975X-RAY DIFFRACTION94
2.0607-2.09010.31374450.27822376X-RAY DIFFRACTION91
2.0901-2.1213000.23442982X-RAY DIFFRACTION94
2.1213-2.1545000.22263042X-RAY DIFFRACTION98
2.1545-2.18980.26364910.20732580X-RAY DIFFRACTION99
2.1898-2.2275000.23212319X-RAY DIFFRACTION97
2.2275-2.2681000.33871572X-RAY DIFFRACTION50
2.2681-2.31170.2893660.27541945X-RAY DIFFRACTION74
2.3117-2.3589000.19953129X-RAY DIFFRACTION98
2.3589-2.4102000.19283093X-RAY DIFFRACTION99
2.4102-2.46620.27443850.18992755X-RAY DIFFRACTION99
2.4662-2.5279000.19913047X-RAY DIFFRACTION99
2.5279-2.59620.25443790.18172698X-RAY DIFFRACTION99
2.5962-2.6726000.19763036X-RAY DIFFRACTION96
2.6726-2.7589000.19632976X-RAY DIFFRACTION96
2.7589-2.85750.25033370.20332719X-RAY DIFFRACTION97
2.8575-2.9719000.19723048X-RAY DIFFRACTION98
2.9719-3.10710.24292970.19152760X-RAY DIFFRACTION96
3.1071-3.2709000.18922972X-RAY DIFFRACTION96
3.2709-3.47570.24162670.17052596X-RAY DIFFRACTION91
3.4757-3.744000.17072461X-RAY DIFFRACTION79
3.744-4.12060.16682220.15172381X-RAY DIFFRACTION82
4.1206-4.71630.16382030.12912749X-RAY DIFFRACTION94
4.7163-5.94020.26341510.14992828X-RAY DIFFRACTION96
5.9402-47.01040.1823780.18672667X-RAY DIFFRACTION87
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)
10.95620.0179-0.11771.98940.15011.66950.01260.06180.0531-0.0730.07260.06330.0302-0.0049-0.05120.14730.00280.00380.1203-0.00770.14250.2163-1.736121.5174
21.64750.0536-0.52261.08390.12911.18880.0776-0.1154-0.04870.07520.0139-0.10330.02890.0579-0.05950.12940.0223-0.03820.145-0.0360.158312.2124-25.25919.9524
31.57480.2972-0.40711.75140.18530.38560.109-0.30090.03730.16970.0386-0.1910.01050.2124-0.09790.1829-0.0618-0.00870.2933-0.0740.1622-18.289-25.942141.2036
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA8 - 188
2X-RAY DIFFRACTION2chain BB9 - 187
3X-RAY DIFFRACTION3chain CC9 - 187

+
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://pdbjlvh1.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