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- PDB-7au7: Crystal structure of Nod Factor Perception ectodomain -

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Basic information

Entry
Database: PDB / ID: 7au7
TitleCrystal structure of Nod Factor Perception ectodomain
ComponentsSerine/threonine receptor-like kinase NFP
KeywordsPLANT PROTEIN / LysM
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases / positive regulation of defense response to oomycetes / regulation of defense response to fungus / nodulation / vacuolar lumen / protein glycosylation / response to molecule of bacterial origin / defense response / protein tyrosine kinase activity / membrane => GO:0016020 ...Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases / positive regulation of defense response to oomycetes / regulation of defense response to fungus / nodulation / vacuolar lumen / protein glycosylation / response to molecule of bacterial origin / defense response / protein tyrosine kinase activity / membrane => GO:0016020 / ATP binding / plasma membrane
Similarity search - Function
Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine receptor-like kinase NFP
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.547 Å
AuthorsGysel, K. / Blaise, M. / Andersen, K.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish National Research FoundationDNRF79 Denmark
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Kinetic proofreading of lipochitooligosaccharides determines signal activation of symbiotic plant receptors.
Authors: Gysel, K. / Laursen, M. / Thygesen, M.B. / Lironi, D. / Bozsoki, Z. / Hjuler, C.T. / Maolanon, N.N. / Cheng, J. / Bjork, P.K. / Vinther, M. / Madsen, L.H. / Rubsam, H. / Muszynski, A. / ...Authors: Gysel, K. / Laursen, M. / Thygesen, M.B. / Lironi, D. / Bozsoki, Z. / Hjuler, C.T. / Maolanon, N.N. / Cheng, J. / Bjork, P.K. / Vinther, M. / Madsen, L.H. / Rubsam, H. / Muszynski, A. / Ghodrati, A. / Azadi, P. / Sullivan, J.T. / Ronson, C.W. / Jensen, K.J. / Blaise, M. / Radutoiu, S. / Stougaard, J. / Andersen, K.R.
History
DepositionNov 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine receptor-like kinase NFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8867
Polymers29,2591
Non-polymers2,6266
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint45 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.410, 98.160, 71.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein / Non-polymers , 2 types, 54 molecules A

#1: Protein Serine/threonine receptor-like kinase NFP / RLK NFP / Nod factor perception protein / Nod-factor receptor 5


Mass: 29259.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: NFP, MTR_5g019040 / Plasmid: pOET4 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q0GXS4, Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 6 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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: obtained synthetically / 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

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Details

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: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Na-acetate * 3H2O, 0.1 M Na-cacodylate pH 6.5, 30% (w/v) PEG-8000,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.547→34.08 Å / Num. obs: 9247 / % possible obs: 79.6 % / Redundancy: 6.74 % / Biso Wilson estimate: 43.85 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.155 / Rrim(I) all: 0.168 / Net I/σ(I): 10.7
Reflection shellResolution: 2.547→2.62 Å / Mean I/σ(I) obs: 1.95 / Num. unique obs: 136 / CC1/2: 0.636 / % possible all: 20

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EBZ

4ebz


Resolution: 2.547→34.08 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 733 9.89 %
Rwork0.205 6675 -
obs0.2112 7408 79.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.88 Å2 / Biso mean: 53.8854 Å2 / Biso min: 15.74 Å2
Refinement stepCycle: final / Resolution: 2.547→34.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1595 0 173 53 1821
Biso mean--86.74 42.77 -
Num. residues----203
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.547-2.74340.3378610.312956434
2.7434-3.01930.38421160.3007112968
3.0193-3.45580.3051780.2301158496
3.4558-4.35260.26551850.1851662100
4.3526-34.080.21811930.17771736100
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)
13.93920.2049-0.71344.7586-0.27484.4527-0.18530.75090.7292-0.0655-0.0852-0.0979-0.13670.02230.10690.1786-0.111-0.04610.28410.09160.274342.171120.600341.5029
25.6419-5.76651.46176.67150.36164.84150.2095-0.0774-1.22890.1989-0.02380.66091.1547-1.20230.36110.5738-0.12410.12220.3006-0.10510.284936.59125.786642.6268
33.76410.4152-0.27381.5427-0.45553.8173-0.11750.82150.8859-0.0658-0.03-0.0614-0.0493-0.25570.07660.164-0.0969-0.01840.40820.18140.276245.55623.028337.2565
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 42 through 91 )A42 - 91
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 105 )A92 - 105
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 244 )A106 - 244

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