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Yorodumi- PDB-4hp0: Crystal Structure of Hen Egg White Lysozyme in complex with GN3-M -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hp0 | |||||||||
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Title | Crystal Structure of Hen Egg White Lysozyme in complex with GN3-M | |||||||||
Components | Lysozyme C | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Lysozyme / Carbohydrate / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å | |||||||||
Authors | Umemoto, N. / Numata, T. / Ohnuma, T. / Fukamizo, T. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: A novel transition-state analogue for lysozyme, 4-O-beta-tri-N-acetylchitotriosyl moranoline, provided evidence supporting the covalent glycosyl-enzyme intermediate. Authors: Ogata, M. / Umemoto, N. / Ohnuma, T. / Numata, T. / Suzuki, A. / Usui, T. / Fukamizo, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hp0.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hp0.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 4hp0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hp0_validation.pdf.gz | 754.6 KB | Display | wwPDB validaton report |
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Full document | 4hp0_full_validation.pdf.gz | 754.6 KB | Display | |
Data in XML | 4hp0_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 4hp0_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/4hp0 ftp://data.pdbj.org/pub/pdb/validation_reports/hp/4hp0 | HTTPS FTP |
-Related structure data
Related structure data | 4hpiC 1bwjS C: citing same article (ref.) 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: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / 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 / triacetyl-beta-chitotriose |
#3: Chemical | ChemComp-NOJ / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Magnesium chloride hexahydrate, 0.1M BIS-TRIS(pH6.5), 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2012 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→54.32 Å / Num. obs: 37127 / % possible obs: 100 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 67.3 |
Reflection shell | Resolution: 1.19→1.21 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 10.6 / Num. unique all: 22214 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BWJ Resolution: 1.19→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.078 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.04 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.551 Å2
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Refinement step | Cycle: LAST / Resolution: 1.19→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.19→1.221 Å / Total num. of bins used: 20
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