+Open data
-Basic information
Entry | Database: PDB / ID: 1at6 | |||||||||
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Title | HEN EGG WHITE LYSOZYME WITH A ISOASPARTATE RESIDUE | |||||||||
Components | LYSOZYME | |||||||||
Keywords | HYDROLASE / ISOASPARTATE / O-GLYCOSYL HYDROLASE | |||||||||
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 | Noguchi, S. / Miyawaki, K. / Satow, Y. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Succinimide and isoaspartate residues in the crystal structures of hen egg-white lysozyme complexed with tri-N-acetylchitotriose. Authors: Noguchi, S. / Miyawaki, K. / Satow, Y. #1: Journal: J.Cryst.Growth / Year: 1996 Title: Crystallography of Succinimide Hen Egg-White Lysozyme at Low Temperatures Authors: Miyawaki, K. / Noguchi, S. / Harada, S. / Satow, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1at6.cif.gz | 40.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1at6.ent.gz | 29.6 KB | Display | PDB format |
PDBx/mmJSON format | 1at6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1at6_validation.pdf.gz | 739.4 KB | Display | wwPDB validaton report |
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Full document | 1at6_full_validation.pdf.gz | 739.4 KB | Display | |
Data in XML | 1at6_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 1at6_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/1at6 ftp://data.pdbj.org/pub/pdb/validation_reports/at/1at6 | HTTPS FTP |
-Related structure data
Related structure data | 1at5C 1lzbS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOASPARTATE AT RESIDUE 101 / Source: (natural) Gallus gallus (chicken) / Cell: EGG / Cellular location: CYTOPLASM (WHITE) / 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: 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: 1.9 Å3/Da / Density % sol: 36 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 7.5 Details: CRYSTALS WERE PREPARED AT 277 K FROM THE DROPLET MIXTURE OF A 20 MG/ML PROTEIN SOLUTION CONTAINING 7 MM TRI-N-ACETYLCHITOTRIOSE (NAG3) AND 50 MM ACETATE BUFFER PH 4.2 WITH EQUAL VOLUME OF A ...Details: CRYSTALS WERE PREPARED AT 277 K FROM THE DROPLET MIXTURE OF A 20 MG/ML PROTEIN SOLUTION CONTAINING 7 MM TRI-N-ACETYLCHITOTRIOSE (NAG3) AND 50 MM ACETATE BUFFER PH 4.2 WITH EQUAL VOLUME OF A RESERVOIR SOLUTION CONTAINING 2.0 M AMMONIUM FORMATE AND 100 MM N-(2-HYDROXYETHYL)PIPERAZINE-N'-(2-ETHANESULFONIC ACID) (HEPES) BUFFER PH 7.5. PRIOR TO THE DIFFRACTION DATA COLLECTION, THE CRYSTAL WAS SOAKED IN A CRYOPROTECTANT SOLUTION CONTAINING 30 % (W/V) POLYETHYLENE GLYCOL 20,000, 2.2 M AMMONIUM FORMATE, 100 MM HEPES BUFFER PH 7.5, AND 7 MM NAG3 FOR 2 MINUTES AT 277 K. PH range: 4.2-7.5 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: unknown | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→34.3 Å / Num. obs: 10515 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 39.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 7.1 / % possible all: 64.9 |
Reflection | *PLUS Num. measured all: 115484 |
Reflection shell | *PLUS % possible obs: 64.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LZB Resolution: 1.8→34.3 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: POSTERIORI / σ(F): 0 Details: A BULK SOLVENT ANALYSIS, WITH MASK PARAMETERS K = 0.350 (ELECTRON/ANGSTROM**3) AND B = 73.6 (ANGSTROM**2), WAS APPLIED IN THE REFINEMENT. ALTHOUGH BOND DISTANCES BETWEEN MET 12 SD AND CE AND ...Details: A BULK SOLVENT ANALYSIS, WITH MASK PARAMETERS K = 0.350 (ELECTRON/ANGSTROM**3) AND B = 73.6 (ANGSTROM**2), WAS APPLIED IN THE REFINEMENT. ALTHOUGH BOND DISTANCES BETWEEN MET 12 SD AND CE AND BETWEEN ARG 14 CG AND CD DEVIATE BY LARGER THAN 4.0*RMSD FROM THE IDEAL VALUES, ALL THE ATOMS OF MET 12 AND ARG 14 ARE DEFINED IN THE ELECTRON DENSITIES.
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Displacement parameters | Biso mean: 14.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→34.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.23 / Lowest resolution: 8 Å / Num. reflection obs: 10348 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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