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- PDB-4b8v: Cladosporium fulvum LysM effector Ecp6 in complex with a beta-1,4... -

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Basic information

Entry
Database: PDB / ID: 4b8v
TitleCladosporium fulvum LysM effector Ecp6 in complex with a beta-1,4- linked N-acetyl-D-glucosamine tetramer
ComponentsEXTRACELLULAR PROTEIN 6
KeywordsSUGAR BINDING PROTEIN / CHITIN / LYSM
Function / homology
Function and homology information


chitin binding / extracellular region
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
Secreted LysM effector ECP6
Similarity search - Component
Biological speciesPASSALORA FULVA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.59 Å
AuthorsSaleem-Batcha, R. / Sanchez-Vallet, A. / Hansen, G. / Thomma, B.P.H.J. / Mesters, J.R.
Citation
Journal: Elife / Year: 2013
Title: Fungal Effector Ecp6 Outcompetes Host Immune Receptor for Chitin Binding Through Intrachain Lysm Dimerization
Authors: Sanchez-Vallet, A. / Saleem-Batcha, R. / Kombrink, A. / Hansen, G. / Valkenburg, D.J. / Thomma, B.P.H.J. / Mesters, J.R.
#1: Journal: Science / Year: 2010
Title: Conserved Fungal Lysm Effector Ecp6 Prevents Chitin-Triggered Immunity in Plants.
Authors: De Jonge, R. / Van Esse, H.P. / Kombrink, A. / Shinya, T. / Desaki, Y. / Bours, R. / Van Der Krol, S. / Shibuya, N. / Joosten, M.H.A.J. / Thomma, B.P.H.J.
History
DepositionAug 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EXTRACELLULAR PROTEIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3694
Polymers23,8921
Non-polymers1,4763
Water2,144119
1
A: EXTRACELLULAR PROTEIN 6
hetero molecules

A: EXTRACELLULAR PROTEIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7378
Polymers47,7842
Non-polymers2,9536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area7560 Å2
ΔGint53.4 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.500, 57.500, 118.730
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 EXTRACELLULAR PROTEIN 6 / FUNGAL EFFECTOR ECP6


Mass: 23892.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PASSALORA FULVA (fungus) / Plasmid: PPIC9 / Production host: KOMAGATAELLA PASTORIS (fungus) / References: UniProt: B3VBK9
#2: 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.: 1
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
#3: 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-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1a_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O]/1-2-2-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#4: 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.: 1
Source method: isolated from a genetically manipulated source
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsGLMU EXISTS AS A BIFUNCTIONAL ENZYME IN MANY BACTERIA INCLUDING MTU, CATALYSING TWO CONSECUTIVE ...GLMU EXISTS AS A BIFUNCTIONAL ENZYME IN MANY BACTERIA INCLUDING MTU, CATALYSING TWO CONSECUTIVE REACTIONS-FIRST, ACETYLTRANSFERASE REACTION CONVERTING ALPHA-D-GLUCOSAMINE-1-PHOSPHATE (GLCN1P)(NAG) TO N-ACETYL-ALPHA-D-GLUCOSAMINE-1-PHOSPHATE (GLCNAC1P)(NDG).

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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: 2.44 Å3/Da / Density % sol: 0.44 % / Description: NONE
Crystal growpH: 4.6
Details: ECP6 IN 20 MM HEPES, PH 7.0, AND 50 MM NACL. CRYSTALS WERE OBTAINED BY MICRO-SEEDING, USING A RESERVOIR WITH 200 MM AMMONIUM SULPHATE, 100 MM SODIUM ACETATE, PH 4.6, AND 20-30% PEG MME 200 (W/V).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91814
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91814 Å / Relative weight: 1
ReflectionResolution: 1.6→49.8 Å / Num. obs: 31231 / % possible obs: 98.1 % / Observed criterion σ(I): -2 / Redundancy: 9.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 7.8
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.59→49.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.523 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22504 1546 5 %RANDOM
Rwork0.20254 ---
obs0.20369 30624 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.975 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.11 Å20 Å2
2---0.21 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.59→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1387 0 99 119 1605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021521
X-RAY DIFFRACTIONr_bond_other_d0.0010.02947
X-RAY DIFFRACTIONr_angle_refined_deg1.8052.0492094
X-RAY DIFFRACTIONr_angle_other_deg1.4483.0072352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.00628.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79715234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211614
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02218
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.592→1.633 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 105 -
Rwork0.24 1850 -
obs--91.91 %
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)
15.1041-1.32161.182210.2068-4.63372.1724-0.0794-0.20930.1190.40970.06580.0021-0.1899-0.0540.01360.08340.0237-0.03160.0434-0.01660.066812.478121.654722.9121
20.59170.0137-0.0544.03640.37760.9510.03250.13660.3184-0.1556-0.0352-0.2514-0.2039-0.06770.00270.07890.03980.01240.09850.06970.191613.610716.923915.1726
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1199 - 1202
2X-RAY DIFFRACTION2A7 - 1198

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