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- PDB-4b9h: Cladosporium fulvum LysM effector Ecp6 in complex with a beta-1,4... -

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Basic information

Entry
Database: PDB / ID: 4b9h
TitleCladosporium fulvum LysM effector Ecp6 in complex with a beta-1,4- linked N-acetyl-D-glucosamine tetramer: I3C heavy atom derivative
ComponentsEXTRACELLULAR PROTEIN 6
KeywordsSUGAR BINDING PROTEIN
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 profile. / LysM domain / LysM domain / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-I3C / Secreted LysM effector ECP6
Similarity search - Component
Biological speciesPASSALORA FULVA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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
DepositionSep 4, 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_leaving_atom_flag / _struct_conn.pdbx_role / _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
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)25,9275
Polymers23,8921
Non-polymers2,0354
Water95553
1
A: EXTRACELLULAR PROTEIN 6
hetero molecules

A: EXTRACELLULAR PROTEIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,85510
Polymers47,7842
Non-polymers4,0708
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area7790 Å2
ΔGint55.6 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.889, 57.889, 119.679
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein EXTRACELLULAR PROTEIN 6 / FUNGAL EFFECTOR ECP6


Mass: 23892.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CLADOSPORIUM FULVUM LYSM EFFECTOR ECP6 IN COMPLEX WITH A BETA-1,4-LINKED N-ACETYL-D-GLUCOSAMINE TETRAMER (CHITIN)
Source: (gene. exp.) PASSALORA FULVA (fungus) / Plasmid: PPIC9 / Production host: KOMAGATAELLA PASTORIS (fungus) / References: UniProt: B3VBK9

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Sugars , 3 types, 3 molecules

#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

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Non-polymers , 2 types, 54 molecules

#5: Chemical ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H4I3NO4
#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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Details

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: 2.42 Å3/Da / Density % sol: 49.2 % / Description: NONE
Crystal growpH: 4.6 / Details: pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.7
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.1→31.2 Å / Num. obs: 13761 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 18.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 44.1
Reflection shellResolution: 2.1→2.63 Å / Redundancy: 18.5 % / Rmerge(I) obs: 0.01 / Mean I/σ(I) obs: 16.5 / % possible all: 99.5

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Processing

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

Resolution: 2.1→50.13 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.923 / SU B: 10.319 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26572 689 5 %RANDOM
Rwork0.21042 ---
obs0.21316 13072 97.24 %-
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: 39.701 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0.45 Å20 Å2
2---0.9 Å20 Å2
3---1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1387 0 115 53 1555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021531
X-RAY DIFFRACTIONr_bond_other_d0.0010.02947
X-RAY DIFFRACTIONr_angle_refined_deg1.9412.0612108
X-RAY DIFFRACTIONr_angle_other_deg1.0213.0072349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3225188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.40628.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60215234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.110.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211622
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02220
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: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 44 -
Rwork0.233 709 -
obs--77.39 %
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)
115.5962-1.74584.39986.2959-2.37621.8236-0.0113-0.41960.20760.3382-0.1036-0.1416-0.1129-0.06940.11490.09450.0226-0.01680.1306-0.02970.1243-12.592821.730662.7378
23.3889-1.3959-0.62571.74690.5751.1232-0.02510.37210.2869-0.1221-0.04240.2827-0.0736-0.23190.06750.114-0.0197-0.0520.17660.05780.1628-7.836920.271455.0824
3124.5397-108.227546.936294.5724-40.623917.7423-1.1443-1.39090.59250.48320.9346-0.5743-0.5898-0.5970.20970.52780.22730.07070.33180.080.33477.043132.698950.311
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1199 - 1202
2X-RAY DIFFRACTION2A7 - 1963
3X-RAY DIFFRACTION3A1203

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