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- PDB-6q40: A secreted LysM effector of the wheat pathogen Zymoseptoria triti... -

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Basic information

Entry
Database: PDB / ID: 6q40
TitleA secreted LysM effector of the wheat pathogen Zymoseptoria tritici protects the fungal hyphae against chitinase hydrolysis through ligand-dependent polymerisation of LysM homodimers
ComponentsLysM domain-containing protein
KeywordsHYDROLASE / Lectin / chitine-binding / oligomerization / protomer / LysM
Function / homology
Function and homology information


defense response to other organism / apoplast / chitin binding
Similarity search - Function
Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Roll / Alpha Beta
Similarity search - Domain/homology
triacetyl-beta-chitotriose / LysM domain-containing protein
Similarity search - Component
Biological speciesZymoseptoria tritici IPO323 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.412 Å
AuthorsMesters, J.R. / Saleem-Batcha, R. / Sanchez-Vallet, A. / Thomma, B.P.H.J.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research Netherlands
Citation
Journal: Plos Pathog. / Year: 2020
Title: A secreted LysM effector protects fungal hyphae through chitin-dependent homodimer polymerization.
Authors: Sanchez-Vallet, A. / Tian, H. / Rodriguez-Moreno, L. / Valkenburg, D.J. / Saleem-Batcha, R. / Wawra, S. / Kombrink, A. / Verhage, L. / de Jonge, R. / van Esse, H.P. / Zuccaro, A. / Croll, D. ...Authors: Sanchez-Vallet, A. / Tian, H. / Rodriguez-Moreno, L. / Valkenburg, D.J. / Saleem-Batcha, R. / Wawra, S. / Kombrink, A. / Verhage, L. / de Jonge, R. / van Esse, H.P. / Zuccaro, A. / Croll, D. / Mesters, J.R. / Thomma, B.P.H.J.
#1: Journal: Biorxiv / Year: 2019
Title: A secreted LysM effector protects fungal hyphae through chitin-dependent homodimer polymerization
Authors: Sanchez-Vallet, A. / Rodriguez-Moreno, L. / Valkenburg, D.-J. / Saleem-Batcha, R. / Wawra, S. / Croll, D. / Mesters, J.R. / Thomma, B.P.H.J.
History
DepositionDec 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author / Item: _chem_comp.type
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LysM domain-containing protein
B: LysM domain-containing protein
C: LysM domain-containing protein
D: LysM domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3408
Polymers34,6064
Non-polymers7344
Water2,342130
1
A: LysM domain-containing protein
B: LysM domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0025
Polymers17,3032
Non-polymers6993
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-29 kcal/mol
Surface area8240 Å2
MethodPISA
2
C: LysM domain-containing protein
D: LysM domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3393
Polymers17,3032
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-14 kcal/mol
Surface area9080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.390, 119.390, 157.670
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-220-

HOH

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Components

#1: Protein
LysM domain-containing protein


Mass: 8651.568 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymoseptoria tritici IPO323 (fungus) / Gene: MYCGRDRAFT_105487 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: F9XHX3
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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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: 4.69 Å3/Da / Density % sol: 73.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein stock: 20 mM HEPES pH 7.0, and 50 mM NaCl Initial crystals: Reservoir 47.5% dioxan Seeds stock for micro-seeding: 45% dioxan Best conditions: By micro-seeding techniques using 0.1 M ...Details: Protein stock: 20 mM HEPES pH 7.0, and 50 mM NaCl Initial crystals: Reservoir 47.5% dioxan Seeds stock for micro-seeding: 45% dioxan Best conditions: By micro-seeding techniques using 0.1 M sodium citrate pH 5.6, 5%-20% PEG4000 and 5% isopropanol as the reservoir solution. Crystal cryo and soaking buffer: 0.2 M sodium acetate pH 4.6 with 20% ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.412→39.452 Å / Num. obs: 26300 / % possible obs: 92.1 % / Redundancy: 10.7 % / Biso Wilson estimate: 43.72 Å2 / Rsym value: 0.083 / Net I/σ(I): 18
Reflection shellResolution: 2.412→2.5086 Å / Num. unique obs: 2827 / % possible all: 100

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Processing

Software
NameClassification
PHENIXphasing
PHENIXrefinement
Cootmodel building
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.412→39.452 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2203 1219 5.06 %
Rwork0.1796 --
obs0.1815 25331 97.13 %
Displacement parametersBiso mean: 55.2 Å2
Refinement stepCycle: LAST / Resolution: 2.412→39.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 46 130 2587

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