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- PDB-28wb: Crystal structure of the STRUBBELIG-RECEPTOR FAMILY 6 (SRF6) ecto... -

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Basic information

Entry
Database: PDB / ID: 28wb
TitleCrystal structure of the STRUBBELIG-RECEPTOR FAMILY 6 (SRF6) ectodomain from Arabidopsis thaliana
ComponentsProtein STRUBBELIG-RECEPTOR FAMILY 6
KeywordsMEMBRANE PROTEIN / receptor kinase / leucine-rich repeat domain / plant cell wall / signal transduction
Function / homology
Function and homology information


protein kinase activity / signal transduction / ATP binding / nucleus / 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 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily ...: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich repeat / 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/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
CITRIC ACID / Protein STRUBBELIG-RECEPTOR FAMILY 6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.501 Å
AuthorsHohmann, U. / Cargenato, A. / Hothorn, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_205201 Switzerland
CitationJournal: To Be Published
Title: Using the ExMatrix crystallization screen to determine the crystal structure of the plant cell wall receptor SRF6 ectodomain.
Authors: Caregnato, A. / Hohmann, U. / Hothorn, M.
History
DepositionFeb 23, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein STRUBBELIG-RECEPTOR FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7664
Polymers28,5281
Non-polymers2383
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-14 kcal/mol
Surface area9650 Å2
Unit cell
Length a, b, c (Å)76.720, 76.720, 86.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

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Components

#1: Protein Protein STRUBBELIG-RECEPTOR FAMILY 6 / Leucine-rich repeat receptor kinase-like protein SRF6


Mass: 28527.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col-0 / Tissue: seedling / Gene: SRF6, At1g53730, F22G10.3, F22G10.31 / Plasmid: pBB3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9C8M9
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 25% PEG3350, 0.2M NaCl, 0.1M citrate pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.977944 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977944 Å / Relative weight: 1
ReflectionResolution: 1.5→45.95 Å / Num. obs: 39355 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.6 % / CC1/2: 0.999 / Rrim(I) all: 0.174 / Net I/σ(I): 13.9
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 1.11 / Num. unique obs: 6330 / CC1/2: 0.508 / Rrim(I) all: 2.58 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.501→45.948 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.559 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.067
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2091 5.002 %RANDOM
Rwork0.1621 39715 --
all0.164 ---
obs-41806 99.926 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.124 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å2-0 Å2-0 Å2
2--0.77 Å2-0 Å2
3----1.539 Å2
Refinement stepCycle: LAST / Resolution: 1.501→45.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 15 237 1947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121816
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161690
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.7782495
X-RAY DIFFRACTIONr_angle_other_deg0.6321.723916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9675251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.8453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1110295
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.8921075
X-RAY DIFFRACTIONr_chiral_restr0.0930.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022173
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02413
X-RAY DIFFRACTIONr_nbd_refined0.2820.2390
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.21657
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2938
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2967
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2149
X-RAY DIFFRACTIONr_metal_ion_refined0.3260.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2710.214
X-RAY DIFFRACTIONr_nbd_other0.1890.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2130.230
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1010.21
X-RAY DIFFRACTIONr_mcbond_it1.8151.832929
X-RAY DIFFRACTIONr_mcbond_other1.8151.832929
X-RAY DIFFRACTIONr_mcangle_it2.5563.2881166
X-RAY DIFFRACTIONr_mcangle_other2.5553.2931167
X-RAY DIFFRACTIONr_scbond_it3.0182.07887
X-RAY DIFFRACTIONr_scbond_other2.9952.066884
X-RAY DIFFRACTIONr_scangle_it4.4953.6851316
X-RAY DIFFRACTIONr_scangle_other4.4933.6841317
X-RAY DIFFRACTIONr_lrange_it6.02221.6822176
X-RAY DIFFRACTIONr_lrange_other6.02221.6812177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.501-1.540.3291500.31928530.31930290.9050.90699.14160.303
1.54-1.5820.2821480.28328050.28329530.9250.9271000.262
1.582-1.6280.2561460.24927640.2529100.9470.9451000.22
1.628-1.6780.281380.23726390.23927770.9390.9541000.207
1.678-1.7330.2471370.21725960.21827330.9520.9631000.185
1.733-1.7940.1911310.19524960.19526270.9720.9721000.162
1.794-1.8610.2291280.17424270.17725550.9650.9781000.14
1.861-1.9370.2041230.16223260.16424490.9740.9821000.132
1.937-2.0230.2241190.1622600.16323790.9680.9831000.129
2.023-2.1220.2041120.15121320.15422440.9760.9851000.126
2.122-2.2360.1821080.14120530.14321610.980.9881000.117
2.236-2.3710.1541020.13619460.13720480.9840.9891000.116
2.371-2.5350.185970.13918310.14119280.9770.9871000.116
2.535-2.7370.183900.13817240.1418140.9790.9881000.117
2.737-2.9970.171840.14115820.14316660.9780.9881000.12
2.997-3.3490.21760.1614490.16215250.9750.9841000.141
3.349-3.8640.172680.14413000.14613680.9840.9871000.134
3.864-4.7240.138580.11911000.1211580.9890.9921000.117
4.724-6.6460.18470.1628860.1639330.9860.9881000.153
6.646-45.9480.226290.1725450.1745750.960.97999.82610.171

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