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Yorodumi- PDB-3mgw: Thermodynamics and structure of a salmon cold-active goose-type l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mgw | ||||||
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Title | Thermodynamics and structure of a salmon cold-active goose-type lysozyme | ||||||
Components | Lysozyme g | ||||||
Keywords | HYDROLASE / Salmon / goose-type / lysozyme / differential scanning calorimetry / refolding / thermal tolerance / innate immunity | ||||||
Function / homology | Function and homology information peptidoglycan catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium Similarity search - Function | ||||||
Biological species | Salmo salar (Atlantic salmon) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Kyomuhendo, P. / Myrnes, B. / Brandsdal, B.O. / Smalas, A.O. / Nilsen, I.W. / Helland, R. | ||||||
Citation | Journal: Comp.Biochem.Physiol. B: Biochem.Mol.Biol. / Year: 2010 Title: Thermodynamics and structure of a salmon cold active goose-type lysozyme Authors: Kyomuhendo, P. / Myrnes, B. / Brandsdal, B.O. / Smalas, A.O. / Nilsen, I.W. / Helland, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mgw.cif.gz | 53.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mgw.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 3mgw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mgw_validation.pdf.gz | 428.7 KB | Display | wwPDB validaton report |
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Full document | 3mgw_full_validation.pdf.gz | 428.8 KB | Display | |
Data in XML | 3mgw_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 3mgw_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/3mgw ftp://data.pdbj.org/pub/pdb/validation_reports/mg/3mgw | HTTPS FTP |
-Related structure data
Related structure data | 153lS 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: 20272.795 Da / Num. of mol.: 1 / Fragment: g-type lysozyme, UNP residues 22-200 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmo salar (Atlantic salmon) / Gene: lysG, LYG / Plasmid: pQE-2 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 (pREP4) / References: UniProt: A6PZ97, lysozyme |
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#2: Chemical | ChemComp-CO / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Sequence details | AUTHOR STATED THAT RESIDUE A133V WAS NOT A INTENTIONA |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.96 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 43-45 % ammonium sulphate, 0.01M cobalt chloride, 0.1M MES , pH 6.25-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K PH range: 6.25-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2007 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→42.76 Å / Num. all: 19410 / Num. obs: 19410 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 20.38 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2840 / Rsym value: 0.49 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 153L Resolution: 1.75→42.76 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.379 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; 2. The polypeptide is traced where electron density is observed, but density for residues 22-24 indicates disorder. There appears to be ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; 2. The polypeptide is traced where electron density is observed, but density for residues 22-24 indicates disorder. There appears to be proteolytic cleavage after residue 21.
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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: 24.55 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→42.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.796 Å / Total num. of bins used: 20
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