[English] 日本語
Yorodumi
- PDB-5ls2: Receptor mediated chitin perception in legumes is functionally se... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ls2
TitleReceptor mediated chitin perception in legumes is functionally seperable from Nod factor perception
ComponentsLysM type receptor kinase
KeywordsPLANT PROTEIN / LysM domain / chitin binding / plant defence
Function / homology
Function and homology information


membrane => GO:0016020 / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
LysM type receptor kinase
Similarity search - Component
Biological speciesLotus japonicus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBozsoki, Z. / Cheng, J. / Feng, F. / Gysel, K. / Andersen, K.R. / Oldroyd, G. / Blaise, M. / Radutoiu, S. / Stougaard, J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Receptor-mediated chitin perception in legume roots is functionally separable from Nod factor perception.
Authors: Bozsoki, Z. / Cheng, J. / Feng, F. / Gysel, K. / Vinther, M. / Andersen, K.R. / Oldroyd, G. / Blaise, M. / Radutoiu, S. / Stougaard, J.
History
DepositionAug 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LysM type receptor kinase
B: LysM type receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,32410
Polymers44,5852
Non-polymers2,7398
Water2,378132
1
A: LysM type receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6625
Polymers22,2931
Non-polymers1,3694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LysM type receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6625
Polymers22,2931
Non-polymers1,3694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.290, 130.690, 53.630
Angle α, β, γ (deg.)90.00, 107.70, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein LysM type receptor kinase


Mass: 22292.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lotus japonicus (plant) / Gene: LYS6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D3KTZ6
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 3.39 Å3/Da / Density % sol: 63.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M ammonium sulfate, 28% peg 2000 MME, 0.1 M sodium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→29.218 Å / Num. obs: 26292 / % possible obs: 100 % / Redundancy: 4.2 % / Biso Wilson estimate: 44.64 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.07
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.8601 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.769 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EBY

4eby


Resolution: 2.3→29.218 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2182 2000 7.61 %
Rwork0.1835 --
obs0.1862 26280 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→29.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3000 0 178 132 3310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023258
X-RAY DIFFRACTIONf_angle_d0.4514467
X-RAY DIFFRACTIONf_dihedral_angle_d11.4221189
X-RAY DIFFRACTIONf_chiral_restr0.056528
X-RAY DIFFRACTIONf_plane_restr0.004571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2998-2.35730.28791420.26641729X-RAY DIFFRACTION100
2.3573-2.4210.30961420.2571723X-RAY DIFFRACTION100
2.421-2.49220.30211420.24591715X-RAY DIFFRACTION100
2.4922-2.57260.31161430.25041739X-RAY DIFFRACTION99
2.5726-2.66450.2651450.23881752X-RAY DIFFRACTION100
2.6645-2.77110.34651400.25091705X-RAY DIFFRACTION100
2.7711-2.89710.25911420.24451727X-RAY DIFFRACTION100
2.8971-3.04970.29781450.23221752X-RAY DIFFRACTION100
3.0497-3.24050.25621430.21081740X-RAY DIFFRACTION100
3.2405-3.49040.22651430.19361736X-RAY DIFFRACTION100
3.4904-3.84090.19081430.16721744X-RAY DIFFRACTION100
3.8409-4.39510.17421420.1421730X-RAY DIFFRACTION100
4.3951-5.53120.16681440.13341741X-RAY DIFFRACTION100
5.5312-29.22080.17111440.1561747X-RAY DIFFRACTION98
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)
14.9994-1.89491.0517.7884-3.31863.25030.1552-0.2092-0.33310.98710.2657-0.09060.01480.4242-0.47190.56470.0283-0.09520.2969-0.05790.420527.7152-15.204573.4216
22.74940.46581.9357.9314-2.01732.3569-0.2202-0.12190.47760.34890.1224-2.18550.07360.94540.07340.5043-0.0045-0.15440.5435-0.0680.702539.0178-15.485772.6717
35.36934.6714-0.2114.9270.57787.0714-0.0496-0.5551-0.14091.4214-0.3504-1.1175-0.53821.08720.32930.9597-0.053-0.41370.6223-0.02020.75436.0743-10.490383.8094
46.69010.0742.89895.6075-3.78259.56380.29460.5404-0.5220.30280.19330.0593-0.58010.5946-0.50040.30240.0984-0.02090.2674-0.0920.389826.7259-14.01667.2725
53.7649-2.98630.08766.5765-0.97292.16070.20980.1364-0.3451-0.1551-0.1843-0.17620.40080.2027-0.01830.4940.0511-0.0640.41-0.0430.427428.9082-24.450167.2465
65.5398-1.0112-1.83025.3471-0.49127.2515-0.0319-0.44360.01010.54810.07470.18220.2429-0.2362-0.04190.5526-0.02560.00130.386-0.01560.355515.9949-13.415281.1677
74.1812-0.1188-0.74516.721-1.68944.4292-0.0247-0.1538-0.21090.32620.0333-0.42150.0077-0.10080.00360.4995-0.0015-0.03930.374-0.04410.300918.8512-10.8576.5203
84.22641.1067-1.46239.0472-5.61525.61320.25480.11310.3553-0.0587-0.03790.537-0.34480.3655-0.23810.4348-0.0351-0.03330.3998-0.08240.390619.18719.054949.7766
96.0915-1.2739-0.52875.9981-2.87314.43490.186-0.2280.9690.9769-0.2963-0.4632-0.91110.6070.05830.6531-0.2577-0.04210.549-0.0160.561426.084517.306152.0642
102.4575-1.24840.08095.2315-2.41366.5473-0.03520.0910.27810.17550.02730.3929-0.3810.1504-0.08820.285-0.0785-0.02070.2977-0.07320.332920.792711.059150.3015
112.526-1.50750.02632.1453-2.11963.74020.17970.04910.70380.81580.31391.3159-1.1772-0.2602-0.36190.8130.00680.10950.48140.03540.89658.025117.06952.7284
122.10150.7345-1.77550.2613-0.64311.6067-0.1451-0.0756-0.15141.06170.47241.5743-0.6313-0.7755-0.12920.52490.09630.27150.54050.15810.96134.97712.617151.6178
132.15230.12290.12953.7652-0.83683.730.11390.12690.3560.04610.04130.701-0.414-0.0811-0.0820.3327-0.02390.01790.31310.01120.435213.78237.024349.1943
146.6391-3.107-0.55917.3543-3.65486.2821-0.13420.30690.0652-0.6658-0.0292-0.45230.40470.64530.18820.3992-0.0062-0.00850.4036-0.06230.307622.7166-3.099838.3265
155.9311-0.91871.00016.4356-1.06575.50370.0385-0.06090.3343-0.2338-0.0913-0.12620.21550.13990.05590.2776-0.0210.05430.3437-0.01420.235421.87880.27145.1246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 61 )
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 97 )
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 165 )
6X-RAY DIFFRACTION6chain 'A' and (resid 166 through 195 )
7X-RAY DIFFRACTION7chain 'A' and (resid 196 through 221 )
8X-RAY DIFFRACTION8chain 'B' and (resid 27 through 46 )
9X-RAY DIFFRACTION9chain 'B' and (resid 47 through 75 )
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 97 )
11X-RAY DIFFRACTION11chain 'B' and (resid 98 through 118 )
12X-RAY DIFFRACTION12chain 'B' and (resid 119 through 137 )
13X-RAY DIFFRACTION13chain 'B' and (resid 138 through 176 )
14X-RAY DIFFRACTION14chain 'B' and (resid 177 through 195 )
15X-RAY DIFFRACTION15chain 'B' and (resid 196 through 222 )

+
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