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- PDB-8jup: Crystal structure of a receptor like kinase from rice -

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Basic information

Entry
Database: PDB / ID: 8jup
TitleCrystal structure of a receptor like kinase from rice
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 / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding ...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 / phosphorylation / 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, 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 ...Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / 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'-TRIPHOSPHATE / 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: 1.98 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

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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)35,7073
Polymers35,1761
Non-polymers5312
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-13 kcal/mol
Surface area13140 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)71,4146
Polymers70,3512
Non-polymers1,0634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area5360 Å2
ΔGint-46 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.140, 71.140, 167.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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: 35175.680 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-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, 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 / Water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.53 Å3/Da / Density % sol: 65.16 %
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: 1.98→19.87 Å / Num. obs: 35135 / % possible obs: 99.9 % / Redundancy: 17.7 % / CC1/2: 0.996 / Net I/σ(I): 9.8
Reflection shellResolution: 1.98→2.03 Å / Num. unique obs: 2556 / CC1/2: 0.715

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Processing

Software
NameVersionClassification
PHENIX(1.15_3459: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→19.28 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 1946 5.67 %
Rwork0.2007 --
obs0.2019 34321 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→19.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 32 247 2467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092258
X-RAY DIFFRACTIONf_angle_d1.1713060
X-RAY DIFFRACTIONf_dihedral_angle_d7.2951340
X-RAY DIFFRACTIONf_chiral_restr0.056354
X-RAY DIFFRACTIONf_plane_restr0.005383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.02950.31961310.27762185X-RAY DIFFRACTION94
2.0295-2.08430.27611370.27982229X-RAY DIFFRACTION96
2.0843-2.14560.28921340.24572232X-RAY DIFFRACTION96
2.1456-2.21470.26011320.23242266X-RAY DIFFRACTION97
2.2147-2.29380.26861370.2392252X-RAY DIFFRACTION96
2.2938-2.38540.23741330.23092258X-RAY DIFFRACTION98
2.3854-2.49380.23531370.21492269X-RAY DIFFRACTION98
2.4938-2.6250.28061420.22082332X-RAY DIFFRACTION98
2.625-2.7890.23271370.21272310X-RAY DIFFRACTION99
2.789-3.00360.2411450.21762343X-RAY DIFFRACTION99
3.0036-3.30450.22031440.20692362X-RAY DIFFRACTION99
3.3045-3.77950.21781460.18222381X-RAY DIFFRACTION100
3.7795-4.750.16991460.15952436X-RAY DIFFRACTION100
4.75-19.280.18831450.18152520X-RAY DIFFRACTION99

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