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- PDB-8peh: Crystal structure of Lotus japonicus SYMRK kinase domain D738N -

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Basic information

Entry
Database: PDB / ID: 8peh
TitleCrystal structure of Lotus japonicus SYMRK kinase domain D738N
ComponentsReceptor-like kinase SYMRK
KeywordsPLANT PROTEIN / Kinase / Symbiosis / Plant / Phosphorylation
Function / homology
Function and homology information


phosphorylation / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding / membrane
Similarity search - Function
Malectin-like domain / Malectin-like domain / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site ...Malectin-like domain / Malectin-like domain / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / 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
non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesLotus japonicus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsNoergaard, M.M.M. / Gysel, K. / Hansen, S.B. / Andersen, K.R.
Funding support Denmark, United States, 2items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF19SA0059362 Denmark
Bill & Melinda Gates FoundationOPP11772165 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Phosphorylation of the alpha-I motif in SYMRK drives root nodule organogenesis.
Authors: Abel, N.B. / Norgaard, M.M.M. / Hansen, S.B. / Gysel, K. / Diez, I.A. / Jensen, O.N. / Stougaard, J. / Andersen, K.R.
History
DepositionJun 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Receptor-like kinase SYMRK
C: Receptor-like kinase SYMRK
A: Receptor-like kinase SYMRK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,82627
Polymers100,8273
Non-polymers2,00024
Water9,206511
1
B: Receptor-like kinase SYMRK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,50211
Polymers33,6091
Non-polymers89310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Receptor-like kinase SYMRK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2089
Polymers33,6091
Non-polymers5998
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Receptor-like kinase SYMRK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1177
Polymers33,6091
Non-polymers5086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.870, 77.960, 101.400
Angle α, β, γ (deg.)90.000, 90.150, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Receptor-like kinase SYMRK


Mass: 33608.977 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lotus japonicus (plant) / Strain: Gifu / Details (production host): T7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: Q8LKX1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS pH 8.5 1.26 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.95→41.59 Å / Num. obs: 80272 / % possible obs: 97.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 34.96 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1228 / Rpim(I) all: 0.05039 / Rrim(I) all: 0.133 / Net I/σ(I): 9.16
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.567 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 7828 / CC1/2: 0.638 / CC star: 0.883 / Rpim(I) all: 0.6385 / Rrim(I) all: 1.695 / % possible all: 95.95

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→41.59 Å / SU ML: 0.2693 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.231 3738 4.66 %
Rwork0.1952 76506 -
obs0.1968 80244 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.97 Å2
Refinement stepCycle: LAST / Resolution: 1.95→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6797 0 111 511 7419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00627088
X-RAY DIFFRACTIONf_angle_d0.77879600
X-RAY DIFFRACTIONf_chiral_restr0.05071052
X-RAY DIFFRACTIONf_plane_restr0.00681228
X-RAY DIFFRACTIONf_dihedral_angle_d12.44762605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.42841100.38752773X-RAY DIFFRACTION95.5
1.97-20.37891410.35672776X-RAY DIFFRACTION96.05
2-2.030.33871450.30882762X-RAY DIFFRACTION96.13
2.03-2.060.29911550.27632815X-RAY DIFFRACTION96.46
2.06-2.090.32061290.26662753X-RAY DIFFRACTION96.42
2.09-2.120.29691460.25282796X-RAY DIFFRACTION96.59
2.12-2.160.29051120.24712826X-RAY DIFFRACTION96.74
2.16-2.190.27381710.24292746X-RAY DIFFRACTION96.43
2.19-2.230.27611270.23692800X-RAY DIFFRACTION96.28
2.23-2.280.25291080.23452821X-RAY DIFFRACTION96.38
2.28-2.320.24911490.22912789X-RAY DIFFRACTION97.58
2.32-2.370.26871510.22692848X-RAY DIFFRACTION97.15
2.37-2.430.31231370.22022805X-RAY DIFFRACTION97.19
2.43-2.490.2591390.21142826X-RAY DIFFRACTION97.56
2.49-2.560.2271500.1912830X-RAY DIFFRACTION97.67
2.56-2.630.25091200.19992844X-RAY DIFFRACTION97.79
2.63-2.720.23081560.19922857X-RAY DIFFRACTION98.05
2.72-2.810.23641200.19472850X-RAY DIFFRACTION98.12
2.81-2.920.20681550.18882842X-RAY DIFFRACTION98.17
2.92-3.060.26711300.20162885X-RAY DIFFRACTION98.3
3.06-3.220.22561420.19292855X-RAY DIFFRACTION98.36
3.22-3.420.23431440.19062887X-RAY DIFFRACTION98.6
3.42-3.680.19631250.17182861X-RAY DIFFRACTION98.58
3.68-4.060.16171620.16252887X-RAY DIFFRACTION98.58
4.06-4.640.23941320.14842896X-RAY DIFFRACTION98.73
4.64-5.840.21171420.17312895X-RAY DIFFRACTION98.13
5.85-41.590.2121400.19352981X-RAY DIFFRACTION98.39
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)
16.9334274277-0.189740530633-2.452498633721.522907846971.218547712023.60256454001-0.2745686943830.688651829356-0.267698655805-0.5318310259520.29118793959-0.2252686832240.3972181757320.364479979953-0.02934317820840.5043461028460.03529703330920.08592572121960.36037930821-0.01011094472860.402079314154-2.20020922159-43.835139767414.7985651768
22.94591185616-0.2871802941990.6481592410752.15885745732-0.3018115564173.39743961024-0.06366601776210.0149010393041-0.03733673581590.01328756508210.0323647755469-0.03582023757220.101593209454-0.05305705153590.03926786085980.206760687757-0.001902445294240.02208617690110.15950159524-0.009617557246180.18353557116-20.8972195258-31.851029562527.3904342431
32.075396086382.420209392342.951458573563.190068970593.552959507164.47887177133-0.0375739964156-0.1384222488150.103614145084-0.0701982488788-0.1837455911240.3268936406860.124313100641-0.4751604595120.2194311941080.353772367113-0.0458463421220.02936154733470.3281414297030.01618204088570.306189464503-42.9854551631-36.7839479773-14.5155346007
42.636037709290.66444888812-0.5609191283852.10267305786-1.728070028525.30403870254-0.06811226896890.0299293841316-0.06671563772-0.179790941436-0.038230724052-0.2350758094350.06687343619930.4739048511810.0787800257420.3166909956480.002146915732570.0002360095550460.280866704595-0.002781839468090.238534796239-22.6480537378-28.0801634327-6.67072042388
55.617493594620.7185699227570.5458943883838.626048669452.474308809036.558327012530.126688974364-0.3191497336080.292560669730.375110251134-0.2558404446010.802187170101-0.129434192491-0.7260515428220.09481890143920.2730404761620.0161815283170.03746839397120.329009530825-0.08602224877940.339541410315-54.0308147663-39.264005201355.2386565653
61.032482935251.509941598850.4476510553384.84324285862.59729365733.976579414960.0552059854172-0.1279049814430.227481851940.0407181679219-0.1240469385660.183107582814-0.286183826235-0.267843131639-0.02004304592840.2516667103590.0529342536042-0.005623981595120.245340520350.02032109558070.278167583116-49.6458722632-49.481754881346.1372218792
75.069539730370.525646318035-3.470486927415.73571322911-1.192768392595.872783180540.0909857593111-0.4656834042260.2263486314520.154827287511-0.0460649133772-0.53292825293-0.3752669254720.156248037601-0.003117031078090.3052848439850.01541797167280.01070690933740.289838274417-0.06814741309140.330784285911-46.7743049711-52.610013864943.405810716
82.466719948250.151759500354-0.9949623748272.70737695226-1.032743240814.037231340390.002031763328340.164204996263-0.0538405704284-0.181079738411-0.014631781521-0.04572894054050.2799293781-0.3330707546580.01252399862310.233990993445-0.01242190627230.0008220850076270.187521874882-0.03864824857570.188421084971-50.3099272014-69.585624549739.3326376012
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 580 through 680 )BA580 - 6801 - 101
22chain 'B' and (resid 681 through 877 )BA681 - 877102 - 290
33chain 'C' and (resid 580 through 741 )CB580 - 7411 - 162
44chain 'C' and (resid 742 through 875 )CB742 - 875163 - 287
55chain 'A' and (resid 578 through 624 )AC578 - 6241 - 47
66chain 'A' and (resid 625 through 709 )AC625 - 70948 - 132
77chain 'A' and (resid 710 through 741 )AC710 - 741133 - 164
88chain 'A' and (resid 758 through 875 )AC758 - 875165 - 282

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