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- PDB-8juv: Crystal structure of a receptor like kinase with ADP -

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Basic information

Entry
Database: PDB / ID: 8juv
TitleCrystal structure of a receptor like kinase with ADP
ComponentsLRR receptor-like serine/threonine-protein kinase FLS2
KeywordsTRANSFERASE / Complex / receptor-like kinase
Function / homology
Function and homology information


defense response by callose deposition in cell wall / detection of bacterium / receptor-mediated endocytosis / non-specific serine/threonine protein kinase / endosome / defense response to bacterium / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / identical protein 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 / Serine/Threonine protein kinases active-site signature. ...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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / LRR receptor-like serine/threonine-protein kinase FLS2
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsMing, Z. / Zhao, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32160064 China
CitationJournal: Plant Commun. / Year: 2024
Title: An active State Formation Mechanism of Receptor Kinase in Plant
Authors: Ming, Z. / Zhao, Q.
History
DepositionJun 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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: LRR receptor-like serine/threonine-protein kinase FLS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0083
Polymers36,5571
Non-polymers4522
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-15 kcal/mol
Surface area13070 Å2
MethodPISA
2
A: LRR receptor-like serine/threonine-protein kinase FLS2
hetero molecules

A: LRR receptor-like serine/threonine-protein kinase FLS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0176
Polymers73,1142
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area4970 Å2
ΔGint-48 kcal/mol
Surface area23020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.315, 72.315, 168.492
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein LRR receptor-like serine/threonine-protein kinase FLS2 / Protein FLAGELLIN-SENSING 2 homolog / OsFLS2 / Protein FLAGELLIN-SENSITIVE 2 homolog


Mass: 36556.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: FLS2, Os04g0618700, LOC_Os04g52780, OsJ_16186 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q0JA29, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.52 Å3/Da / Density % sol: 65.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M lithium sulfate monohydrate, 0.1 M BIS-TRIS (pH 6.5), 25% (w/v) polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.09→62.63 Å / Num. obs: 28589 / % possible obs: 92.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 24.3 Å2 / CC1/2: 0.994 / Net I/σ(I): 13
Reflection shellResolution: 2.09→2.21 Å / Num. unique obs: 3042 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PHENIX1.15_3459refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→31.31 Å / SU ML: 0.1682 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8289
RfactorNum. reflection% reflection
Rfree0.2084 2001 7.02 %
Rwork0.1813 26494 -
obs0.1832 28495 92.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.44 Å2
Refinement stepCycle: LAST / Resolution: 2.09→31.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 0 236 2452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792255
X-RAY DIFFRACTIONf_angle_d0.95473056
X-RAY DIFFRACTIONf_chiral_restr0.0519354
X-RAY DIFFRACTIONf_plane_restr0.0048384
X-RAY DIFFRACTIONf_dihedral_angle_d8.95551339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.2785980.22281285X-RAY DIFFRACTION64.12
2.14-2.20.22121150.20791472X-RAY DIFFRACTION72.8
2.2-2.270.24151300.1881627X-RAY DIFFRACTION80.52
2.27-2.340.24371370.1921817X-RAY DIFFRACTION89.59
2.34-2.420.20321410.19061934X-RAY DIFFRACTION95.49
2.42-2.520.1961490.1921957X-RAY DIFFRACTION97.45
2.52-2.640.22831500.19041980X-RAY DIFFRACTION97.93
2.64-2.780.20851560.18492034X-RAY DIFFRACTION98.65
2.78-2.950.21961540.17892022X-RAY DIFFRACTION99.41
2.95-3.180.19891460.18282023X-RAY DIFFRACTION98.73
3.18-3.50.19291530.18232041X-RAY DIFFRACTION98.78
3.5-40.18191590.15522053X-RAY DIFFRACTION98.53
4-5.040.19051530.15872070X-RAY DIFFRACTION98.62
5.04-31.310.23451600.20212179X-RAY DIFFRACTION97.58

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