[English] 日本語
Yorodumi
- PDB-1dcf: CRYSTAL STRUCTURE OF THE RECEIVER DOMAIN OF THE ETHYLENE RECEPTOR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dcf
TitleCRYSTAL STRUCTURE OF THE RECEIVER DOMAIN OF THE ETHYLENE RECEPTOR OF ARABIDOPSIS THALIANA
ComponentsETR1 PROTEIN
KeywordsTRANSFERASE / BETA-ALPHA FIVE SANDWICH
Function / homology
Function and homology information


ethylene receptor activity / regulation of seedling development / detection of ethylene stimulus / ethylene binding / defense response by callose deposition in cell wall / seed dormancy process / negative regulation of ethylene-activated signaling pathway / sugar mediated signaling pathway / response to gibberellin / response to insect ...ethylene receptor activity / regulation of seedling development / detection of ethylene stimulus / ethylene binding / defense response by callose deposition in cell wall / seed dormancy process / negative regulation of ethylene-activated signaling pathway / sugar mediated signaling pathway / response to gibberellin / response to insect / phloem or xylem histogenesis / response to ethylene / cytokinin metabolic process / regulation of stomatal movement / response to auxin / protein histidine kinase activity / response to abscisic acid / hydrogen peroxide biosynthetic process / histidine kinase / phosphorelay sensor kinase activity / response to salt stress / defense response / response to molecule of bacterial origin / response to heat / defense response to bacterium / cell division / endoplasmic reticulum membrane / endoplasmic reticulum / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
Ethylene receptor / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain ...Ethylene receptor / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / GAF domain / CheY-like superfamily / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Response regulator / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsMuller-Dieckmann, H.J. / Grantz, A. / Kim, S.H.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The structure of the signal receiver domain of the Arabidopsis thaliana ethylene receptor ETR1.
Authors: Muller-Dieckmann, H.J. / Grantz, A.A. / Kim, S.H.
History
DepositionNov 4, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 14, 2016Group: Other
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ETR1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,3051
Polymers15,3051
Non-polymers00
Water73941
1
A: ETR1 PROTEIN

A: ETR1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)30,6102
Polymers30,6102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)47.92, 47.92, 111.79
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein ETR1 PROTEIN


Mass: 15304.866 Da / Num. of mol.: 1 / Fragment: RECEIVER DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli)
References: UniProt: P49333, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.1 Å3/Da / Density % sol: 63.4983 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Li2SO4, HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
122 mg/mlprotein1drop
21.6 M1reservoirLi2SO4
30.1 MHEPES1reservoir
40.03 %1reservoirNaN3

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 5, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 14608 / Num. obs: 4410 / % possible obs: 87 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 69 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.423 / % possible all: 93.5
Reflection shell
*PLUS
% possible obs: 93.5 %

-
Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
SCALEPACKdata scaling
RefinementResolution: 2.5→500 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: engh & huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 455 -random
Rwork0.222 ---
all0.227 4928 --
obs0.227 4324 87.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.815 Å20 Å20 Å2
2---5.815 Å20 Å2
3---11.63 Å2
Refinement stepCycle: LAST / Resolution: 2.5→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 0 0 41 1061
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0065
X-RAY DIFFRACTIONc_angle_deg1.433
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 59 Å2

+
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