+Open data
-Basic information
Entry | Database: PDB / ID: 1v7s | ||||||
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Title | Triclinic hen lysozyme crystallized at 313K from a D2O solution | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / atomic resolution | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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: 1.14 Å | ||||||
Authors | Harata, K. / Akiba, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Phase transition of triclinic hen egg-white lysozyme crystal associated with sodium binding. Authors: Harata, K. / Akiba, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v7s.cif.gz | 71.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v7s.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 1v7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/1v7s ftp://data.pdbj.org/pub/pdb/validation_reports/v7/1v7s | 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: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme | ||
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#2: Chemical | ChemComp-NO3 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.56 Å3/Da / Density % sol: 20.36 % |
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Crystal grow | Temperature: 313 K / Method: evaporation, recrystallization / pH: 4.5 Details: sodium nitrate, sodium acetate, pH 4.5, EVAPORATION, RECRYSTALLIZATION, temperature 313K |
-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Mar 6, 2001 / Details: Confocal Max-Flux |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→17.09 Å / Num. all: 38234 / Num. obs: 36551 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.49 % / Rmerge(I) obs: 0.038 |
Reflection shell | Resolution: 1.14→1.16 Å / Rmerge(I) obs: 0.08 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→17.09 Å / Num. parameters: 10794 / Num. restraintsaints: 12850 / σ(F): 0
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Solvent computation | Solvent model: Moews & Kretsinger | |||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 4 / Occupancy sum hydrogen: 959 / Occupancy sum non hydrogen: 1150.14 | |||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.14→17.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.13→1.18 Å /
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