[English] 日本語
Yorodumi
- PDB-9gfz: Crystal structure of Medicago Truncatula LYK3 kinase domain D459N -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gfz
TitleCrystal structure of Medicago Truncatula LYK3 kinase domain D459N
ComponentsLysM domain receptor-like kinase 3
KeywordsPLANT PROTEIN / Receptor kinase / root nodule symbiosis / RLK/Pelle
Function / homology
Function and homology information


transmembrane receptor protein kinase activity / nodulation / response to symbiotic bacterium / vacuolar lumen / kinase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity ...transmembrane receptor protein kinase activity / nodulation / response to symbiotic bacterium / vacuolar lumen / kinase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
LysM domain / : / LYK3/4/5 LysM2 domain / LysM domain receptor kinase CERK1/LYK3-like / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...LysM domain / : / LYK3/4/5 LysM2 domain / LysM domain receptor kinase CERK1/LYK3-like / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / LysM domain receptor-like kinase 3
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSimonsen, B. / Gysel, K. / Andersen, C.G. / Andersen, K.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF18OC0052855 Denmark
CitationJournal: Biorxiv / Year: 2024
Title: Two residues reprogram immunity receptor kinases to signal in nitrogen-fixing symbiosis
Authors: Tsitsikli, M. / Simonsen, B.W. / Larsen, M.M. / Andersen, C.G. / Gysel, K. / Lironi, D. / Kronauer, C. / Rubsam, H. / Luu, T.B. / Hansen, S.B. / Kaya, G. / Stougaard, J. / Andersen, K.R. / Radutoiu, S.
History
DepositionAug 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Structure summary / Category: audit_author

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LysM domain receptor-like kinase 3
B: LysM domain receptor-like kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4943
Polymers65,9882
Non-polymers5061
Water81145
1
A: LysM domain receptor-like kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5002
Polymers32,9941
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LysM domain receptor-like kinase 3


Theoretical massNumber of molelcules
Total (without water)32,9941
Polymers32,9941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.980, 59.840, 61.240
Angle α, β, γ (deg.)99.905, 105.750, 119.799
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein LysM domain receptor-like kinase 3 / LysM-containing receptor-like kinase 3 / MtLYK3 / LysM receptor kinase K1B / Protein HAIR CURLING


Mass: 32994.051 Da / Num. of mol.: 2 / Mutation: D459N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: LYK3, HCL, RLK3, MTR_5g086130 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6UD73, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium Formate, 0.1 M Bis-Tris propane pH 8.5, 20% w/v PEG 3350, 6 mM AMP-PNP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→42.99 Å / Num. obs: 20193 / % possible obs: 99.76 % / Redundancy: 6.9 % / Biso Wilson estimate: 58.72 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.46
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.11 / Num. unique obs: 1443 / CC1/2: 0.683 / % possible all: 99.24

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→42.99 Å / SU ML: 0.3681 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.4186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2568 1996 9.9 %
Rwork0.2062 18162 -
obs0.2111 20158 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.79 Å2
Refinement stepCycle: LAST / Resolution: 2.5→42.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4467 0 31 45 4543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00154584
X-RAY DIFFRACTIONf_angle_d0.42036206
X-RAY DIFFRACTIONf_chiral_restr0.0393709
X-RAY DIFFRACTIONf_plane_restr0.0029783
X-RAY DIFFRACTIONf_dihedral_angle_d11.62231720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.36621420.35271295X-RAY DIFFRACTION99.1
2.56-2.630.34671410.31851281X-RAY DIFFRACTION99.86
2.63-2.710.33081450.2821312X-RAY DIFFRACTION99.39
2.71-2.80.36961440.2621305X-RAY DIFFRACTION99.79
2.8-2.90.31781420.2721289X-RAY DIFFRACTION100
2.9-3.010.32171410.27311288X-RAY DIFFRACTION99.79
3.01-3.150.30091450.24571325X-RAY DIFFRACTION99.66
3.15-3.320.29261420.23861288X-RAY DIFFRACTION99.65
3.32-3.520.30421420.2181288X-RAY DIFFRACTION99.86
3.52-3.790.2761420.19291290X-RAY DIFFRACTION99.93
3.8-4.180.21771420.16931298X-RAY DIFFRACTION100
4.18-4.780.2071440.16611313X-RAY DIFFRACTION100
4.78-6.020.23031420.19741290X-RAY DIFFRACTION100
6.02-42.990.21531420.17611300X-RAY DIFFRACTION99.52
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)
18.52267995972-0.5895362145995.262149542167.525995443354.02658929257.50461734430.1910228258661.22664219224-0.00501287253244-1.149888392120.2594478792330.4661525416130.8439360365430.459593709663-0.4538156320831.06011228897-0.2576995943260.01465195703910.7851593733310.1468166568690.6370691324937.32418458368-24.306381332-25.9488165859
24.37071982214-0.608736486491-0.4315529971364.81516680313-1.191652540825.127738619720.0564825639885-0.06264947680110.164363079360.02662969786980.07438300736690.251063050539-0.204574385311-0.119076820169-0.1106480135250.453468431183-0.06620812201670.02191799262360.3683626487-0.01076039056580.25622868903615.3739747538-0.330198419987-18.2986834154
35.228417509943.332426062933.102266515324.77386492092-1.130776835975.76188063848-0.002721870261630.287021124103-1.26594212663-0.7368091973740.364870538063-0.2960703262821.36035549477-0.292397075748-0.4220843460161.198427208430.024734374280.2396293895050.849699973915-0.2096903670570.77614201190617.5150988846-37.438872268-0.00169333292423
46.395022810830.2084125511010.7572365425994.06725474463-1.808445634486.09522746361-0.0455168933114-0.143741111499-0.0738329179066-0.030290901411-0.21106843337-0.3276494660820.0106210356770.7365409996150.1794773697390.463256703633-0.001230089750160.03111368991380.4777381415450.05037500300650.31763461772223.2017878106-18.126697546312.2429329759
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 302 through 391 )AA302 - 3911 - 90
22chain 'A' and (resid 392 through 596 )AA392 - 59691 - 288
33chain 'B' and (resid 307 through 411 )BC307 - 4111 - 105
44chain 'B' and (resid 412 through 596 )BC412 - 596106 - 281

+
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