[English] 日本語
Yorodumi
- PDB-9gxz: Structure of the Medicago truncatula LYR4 ectodomain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gxz
TitleStructure of the Medicago truncatula LYR4 ectodomain
ComponentsLysM-domain receptor-like kinase
KeywordsPLANT PROTEIN
Function / homology
Function and homology information


protein kinase activity / ATP binding / membrane
Similarity search - Function
: / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
LysM-domain receptor-like kinase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRuebsam, H. / Gysel, K. / Andersen, K.R.
Funding support Denmark, 3items
OrganizationGrant numberCountry
The Carlsberg Foundation Denmark
Danish Council for Independent Research Denmark
Novo Nordisk Foundation Denmark
CitationJournal: To Be Published
Title: Structural basis for size-selective perception of chitin in plants
Authors: Gysel, K. / Hansen, S.B. / Ruebsam, H. / Alsarraf, H.M.A.B. / Madland, E. / Cheng, J.X.J. / Baadegaard, C. / Poulsen, E.C. / Vinther, M. / Fort, S. / Stougaard, J. / Andersen, K.R.
History
DepositionOct 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LysM-domain receptor-like kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,65922
Polymers27,2301
Non-polymers2,42821
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-6 kcal/mol
Surface area10780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.247, 80.438, 46.898
Angle α, β, γ (deg.)90.000, 90.310, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein LysM-domain receptor-like kinase


Mass: 27230.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11433363, MTR_5g085790, MtrunA17_Chr5g0439331 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G7K7K0
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2M Ammonium sulfate, 0.1 M Bis-Tris buffer pH 5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→40.22 Å / Num. obs: 37799 / % possible obs: 98.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.84 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.22
Reflection shellResolution: 1.5→1.554 Å / Num. unique obs: 3459 / CC1/2: 0.453

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→40.22 Å / SU ML: 0.1742 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.4622
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1833 1887 4.98 %
Rwork0.1464 35999 -
obs0.1483 37797 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.89 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 149 237 2108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01581963
X-RAY DIFFRACTIONf_angle_d1.44262688
X-RAY DIFFRACTIONf_chiral_restr0.1231331
X-RAY DIFFRACTIONf_plane_restr0.0107338
X-RAY DIFFRACTIONf_dihedral_angle_d14.943737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.29611360.2692464X-RAY DIFFRACTION87.6
1.54-1.580.26541340.2362692X-RAY DIFFRACTION96.85
1.58-1.630.25791500.19922802X-RAY DIFFRACTION99.9
1.63-1.690.22531320.17422813X-RAY DIFFRACTION99.76
1.69-1.760.23251630.1642762X-RAY DIFFRACTION99.8
1.76-1.840.2151520.16242783X-RAY DIFFRACTION99.9
1.84-1.940.18681520.12832801X-RAY DIFFRACTION99.8
1.94-2.060.17211470.11882814X-RAY DIFFRACTION99.83
2.06-2.220.1831260.11962800X-RAY DIFFRACTION99.93
2.22-2.440.15251530.12892805X-RAY DIFFRACTION99.56
2.44-2.790.18721580.14282784X-RAY DIFFRACTION99.53
2.8-3.520.16131340.14512841X-RAY DIFFRACTION99.66
3.52-40.220.16541500.14252838X-RAY DIFFRACTION99.37

+
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