[English] 日本語
Yorodumi
- PDB-4mtx: Structure of the ERS1 dimerization and histidine phosphotransfer ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mtx
TitleStructure of the ERS1 dimerization and histidine phosphotransfer domain from Arabidopsis thaliana
ComponentsEthylene response sensor 1
KeywordsTRANSFERASE / Four helix bundle / Histidine kinase / CTR1 / ER MEMBRANE
Function / homology
Function and homology information


ethylene binding / negative regulation of ethylene-activated signaling pathway / ethylene-activated signaling pathway / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / protein histidine kinase activity / histidine kinase / phosphorelay sensor kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / endoplasmic reticulum ...ethylene binding / negative regulation of ethylene-activated signaling pathway / ethylene-activated signaling pathway / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / protein histidine kinase activity / histidine kinase / phosphorelay sensor kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / endoplasmic reticulum / ATP binding / metal ion binding
Similarity search - Function
Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / 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. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. ...Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / 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. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ethylene response sensor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / UV-RIP / Resolution: 2.15 Å
AuthorsMayerhofer, H. / Mueller-Dieckmann, J.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Model of the Cytosolic Domain of the Plant Ethylene Receptor 1 (ETR1).
Authors: Mayerhofer, H. / Panneerselvam, S. / Kaljunen, H. / Tuukkanen, A. / Mertens, H.D. / Mueller-Dieckmann, J.
History
DepositionSep 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Mar 18, 2015Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ethylene response sensor 1
B: Ethylene response sensor 1
C: Ethylene response sensor 1
D: Ethylene response sensor 1


Theoretical massNumber of molelcules
Total (without water)47,1294
Polymers47,1294
Non-polymers00
Water3,171176
1
A: Ethylene response sensor 1
B: Ethylene response sensor 1


Theoretical massNumber of molelcules
Total (without water)23,5652
Polymers23,5652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-47 kcal/mol
Surface area11790 Å2
MethodPISA
2
C: Ethylene response sensor 1
D: Ethylene response sensor 1


Theoretical massNumber of molelcules
Total (without water)23,5652
Polymers23,5652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-52 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.911, 69.193, 108.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

21A-522-

HOH

31C-537-

HOH

41D-514-

HOH

51D-515-

HOH

Detailsasymmetric dimer

-
Components

#1: Protein
Ethylene response sensor 1 / AtERS1 / Protein ERS1


Mass: 11782.331 Da / Num. of mol.: 4
Fragment: dimerization and histidine phosphotransfer domain residues 308-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g40940, ERS, ERS1, T20B5.14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q38846, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases, histidine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.18 M L-proline, 0.1 M HEPES pH 7.5, 9% PEG 3350, 0.12 M sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9919 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2009
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.15→47.7 Å / Num. all: 27660 / Num. obs: 27137 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.15→2.227 Å / % possible all: 99.7

-
Processing

Software
NameVersionClassification
DNAdata collection
SHELXmodel building
PHENIX(phenix.refine: dev_1092)refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: UV-RIP / Resolution: 2.15→47.7 Å / SU ML: 0.24 / σ(F): 1.35 / Phase error: 24.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 1333 4.89 %Random
Rwork0.1984 ---
obs0.2009 27248 98.55 %-
all-27650 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3017 0 0 176 3193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093080
X-RAY DIFFRACTIONf_angle_d1.2084155
X-RAY DIFFRACTIONf_dihedral_angle_d15.3041197
X-RAY DIFFRACTIONf_chiral_restr0.077510
X-RAY DIFFRACTIONf_plane_restr0.005532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.22680.29731260.23132601X-RAY DIFFRACTION100
2.2268-2.3160.281340.21252568X-RAY DIFFRACTION100
2.316-2.42140.29741400.20672566X-RAY DIFFRACTION100
2.4214-2.54910.27111260.20162612X-RAY DIFFRACTION100
2.5491-2.70880.26311260.20542615X-RAY DIFFRACTION100
2.7088-2.91790.28531320.21342600X-RAY DIFFRACTION100
2.9179-3.21140.24281440.20822563X-RAY DIFFRACTION99
3.2114-3.6760.27181270.1912631X-RAY DIFFRACTION98
3.676-4.63080.20761400.1662578X-RAY DIFFRACTION97
4.6308-47.73590.23181380.21122581X-RAY DIFFRACTION92
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)
1-0.0261-0.0951-0.26240.03180.38811.50230.26810.28460.0168-0.172-0.0404-0.0025-0.5018-0.26070.08610.41290.1979-0.0210.42060.01190.2271-4.164123.4333-12.0144
21.1185-0.1076-0.23490.64770.03030.35520.05610.1976-0.0940.06040.0701-0.43910.31240.12310.14070.26720.015-0.02990.0176-0.01390.29758.312824.001818.472
30.14090.1261-0.01650.3340.26540.33250.14520.56610.1844-0.075-0.19280.02360.37450.5312-0.02210.33150.21270.0180.68440.01310.2651.363218.3533-27.0127
42.5153-0.5113-0.32131.175-0.470.32930.06970.5673-0.25450.073-0.1147-0.14780.3310.01820.05120.1891-0.0274-0.0396-0.08640.03450.1655-0.84220.427319.1116
5-0.04870.01810.21010.03190.08831.96020.0651-0.09640.01070.00160.1503-0.03970.33460.42880.01220.24220.0247-0.03050.4011-0.01730.252716.232712.373267.1072
61.5807-0.3184-1.03841.21260.18110.858-0.0951-0.4217-0.06230.38670.00970.11820.16830.1322-0.08690.3282-0.0773-0.0349-0.06020.01240.14694.769811.522337.2772
70.35720.49171.32610.39151.41284.5650.0305-0.32440.0841-0.0338-0.21210.0986-0.0562-0.9969-0.03130.29410.0838-0.02140.39970.01080.28817.849111.409867.784
81.2685-0.10720.27751.0072-0.01991.9835-0.1035-0.24490.04060.1996-0.069-0.24290.00110.4785-0.08470.15410.0406-0.02150.24230.04110.290712.73362.615637.8112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 310:371 )A310 - 371
2X-RAY DIFFRACTION2( CHAIN A AND RESID 372:405 )A372 - 405
3X-RAY DIFFRACTION3( CHAIN B AND RESID 310:350 )B310 - 350
4X-RAY DIFFRACTION4( CHAIN B AND RESID 351:405 )B351 - 405
5X-RAY DIFFRACTION5( CHAIN C AND RESID 310:371 )C310 - 371
6X-RAY DIFFRACTION6( CHAIN C AND RESID 372:406 )C372 - 406
7X-RAY DIFFRACTION7( CHAIN D AND RESID 310:371 )D310 - 371
8X-RAY DIFFRACTION8( CHAIN D AND RESID 372:404 )D372 - 404

+
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