+Open data
-Basic information
Entry | Database: PDB / ID: 2war | |||||||||
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Title | Hen Egg White Lysozyme E35Q chitopentaose complex | |||||||||
Components | LYSOZYME C | |||||||||
Keywords | HYDROLASE / ANTIMICROBIAL / BACTERIOLYTIC ENZYME / ALLERGEN / GLYCOSIDASE | |||||||||
Function / homology | Function and homology information Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | GALLUS GALLUS (chicken) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Davies, G.J. / Withers, S.G. / Vocadlo, D.J. | |||||||||
Citation | Journal: Aust.J.Chem. / Year: 2009 Title: The Chitopentaose Complex of a Mutant Hen Egg-White Lysozyme Displays No Distortion of the -1 Sugar Away from a 4C1 Chair Conformation Authors: Davies, G.J. / Withers, S.G. / Vocadlo, D.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2war.cif.gz | 43.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2war.ent.gz | 29.3 KB | Display | PDB format |
PDBx/mmJSON format | 2war.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2war_validation.pdf.gz | 691.1 KB | Display | wwPDB validaton report |
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Full document | 2war_full_validation.pdf.gz | 691.6 KB | Display | |
Data in XML | 2war_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 2war_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/2war ftp://data.pdbj.org/pub/pdb/validation_reports/wa/2war | HTTPS FTP |
-Related structure data
Related structure data | 1h6mS S: Starting model for refinement |
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Similar 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: 14330.176 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: COMPLEX WITH CHITOPENTAOSE / Source: (gene. exp.) GALLUS GALLUS (chicken) / Tissue: EGG WHITE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00698, lysozyme | ||
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#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-(1-4)-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: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | SITE DIRECTED VARIANT E35Q | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.7 Å3/Da / Density % sol: 27.3 % Description: THE STRUCTURE OF AN APO E35Q LYSOZYME,UNPUBLISHED, WAS USED AS THE STARTING MODEL. THE CLOSEST PUBLISHED, COORDINATES TO THESE ARE 1H6M, ABOVE |
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Crystal grow | pH: 4.5 Details: PROTEIN AT 7MG ML-1 IN 10MM CHITOPENTAOSE 200MM NA ACETATE PH5 WAS MIXED WITH RESERVOIR OF 200MM NA ACETATE, 4% W/V NACL PH4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. obs: 11116 / % possible obs: 93 % / Observed criterion σ(I): -5 / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 40 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 6.4 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H6M Resolution: 1.8→14.76 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.312 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.13 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→14.76 Å
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