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Yorodumi- PDB-4b8v: Cladosporium fulvum LysM effector Ecp6 in complex with a beta-1,4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b8v | |||||||||
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Title | Cladosporium fulvum LysM effector Ecp6 in complex with a beta-1,4- linked N-acetyl-D-glucosamine tetramer | |||||||||
Components | EXTRACELLULAR PROTEIN 6Glossary of biology | |||||||||
Keywords | SUGAR BINDING PROTEIN / CHITIN / LYSM | |||||||||
Function / homology | Function and homology information 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 | |||||||||
Biological species | PASSALORA FULVA (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.59 Å | |||||||||
Authors | Saleem-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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b8v.cif.gz | 87.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b8v.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 4b8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/4b8v ftp://data.pdbj.org/pub/pdb/validation_reports/b8/4b8v | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#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 Source method: isolated from a genetically manipulated source |
#4: Sugar | ChemComp-NAG / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | GLMU EXISTS AS A BIFUNCTIONAL ENZYME IN MANY BACTERIA INCLUDING MTU, CATALYSING TWO CONSECUTIVE ...GLMU EXISTS AS A BIFUNCTION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 0.44 % / Description: NONE |
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Crystal grow | pH: 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). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91814 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91814 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.59→1.68 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / % possible all: 94.1 |
-Processing
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Refinement | Method 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.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.975 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→49.8 Å
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Refine LS restraints |
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