[English] 日本語
Yorodumi
- PDB-3kl1: Crystal structure of abscisic acid receptor PYL2 at 1.55 A -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
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

-
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

-
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

+
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