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- PDB-7brc: Crystal structure of the TMK3 LRR domain -

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Basic information

Entry
Database: PDB / ID: 7brc
TitleCrystal structure of the TMK3 LRR domain
ComponentsReceptor-like kinase TMK3
KeywordsTRANSFERASE / LRR / RLK / TMK / extracellular domain / PLANT PROTEIN
Function / homology
Function and homology information


plant-type cell wall / pollen development / plasmodesma / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine/threonine-protein kinase, active site ...: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / 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
Receptor-like kinase TMK3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsChen, H. / Kong, Y.Q. / Chen, J. / Li, L. / Li, X.S. / Yu, F. / Ming, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31700052 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of the extracellular domain of the receptor-like kinase TMK3 from Arabidopsis thaliana.
Authors: Chen, H. / Kong, Y. / Chen, J. / Li, L. / Li, X. / Yu, F. / Ming, Z.
History
DepositionMar 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-like kinase TMK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2715
Polymers48,9801
Non-polymers1,2914
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint18 kcal/mol
Surface area18710 Å2
Unit cell
Length a, b, c (Å)49.340, 115.610, 57.860
Angle α, β, γ (deg.)90.000, 92.349, 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

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Components

#1: Protein Receptor-like kinase TMK3 / BARK1-like kinase 2 / Leucine-rich repeat receptor-like kinases TMK3 / Transmembrane kinase 3


Mass: 48980.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TMK3, BLK2, At2g01820, T23K3.1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9SIT1, non-specific serine/threonine protein kinase
#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.: 2
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: 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.: 2
Source method: isolated from a genetically manipulated source
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.46 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 4.6
Details: 0.2 M ammonium sulfate, 0.1M sodium acetate trihydrate pH 4.6, 30% W/V PEG monomethyl ether 2000, 0.05 M sodium fluoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979183 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.06→57.81 Å / Num. obs: 39810 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 30.44 Å2 / CC1/2: 0.994 / Net I/σ(I): 10.6
Reflection shellResolution: 2.06→2.11 Å / Num. unique obs: 2890 / CC1/2: 0.666

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HQ1

4hq1


Resolution: 2.06→38.29 Å / SU ML: 0.2335 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.4015
RfactorNum. reflection% reflection
Rfree0.2058 1951 5 %
Rwork0.1769 --
obs0.1783 39030 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.01 Å2
Refinement stepCycle: LAST / Resolution: 2.06→38.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 84 352 3647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00863350
X-RAY DIFFRACTIONf_angle_d0.93214561
X-RAY DIFFRACTIONf_chiral_restr0.0534563
X-RAY DIFFRACTIONf_plane_restr0.0053585
X-RAY DIFFRACTIONf_dihedral_angle_d8.9551474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.110.35121340.30312475X-RAY DIFFRACTION92.13
2.11-2.170.26441410.23082589X-RAY DIFFRACTION96.26
2.17-2.230.23621300.21382628X-RAY DIFFRACTION96.1
2.23-2.30.2811320.23822503X-RAY DIFFRACTION92.78
2.3-2.390.23341370.18392646X-RAY DIFFRACTION97.86
2.39-2.480.19871380.17912697X-RAY DIFFRACTION98.37
2.48-2.60.23571440.1762642X-RAY DIFFRACTION98.1
2.6-2.730.20521410.17762680X-RAY DIFFRACTION98.57
2.73-2.90.18621420.17572695X-RAY DIFFRACTION99.4
2.9-3.130.24751430.18292674X-RAY DIFFRACTION99.3
3.13-3.440.20771360.17222695X-RAY DIFFRACTION99.09
3.44-3.940.16651450.15172708X-RAY DIFFRACTION99.3
3.94-4.960.16721430.13832731X-RAY DIFFRACTION99.69
4.96-38.290.19951450.18822716X-RAY DIFFRACTION98.62

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