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Yorodumi- PDB-2gv0: The structure of the orthorhombic form of soft-shelled turtle lys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gv0 | ||||||
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Title | The structure of the orthorhombic form of soft-shelled turtle lysozyme at 1.9 angstroms resolution | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / LYSOZYME | ||||||
Function / homology | Function and homology information cytolysis / metabolic process / lysozyme / lysozyme activity / defense response to bacterium / extracellular region Similarity search - Function | ||||||
Biological species | Pelodiscus sinensis (Chinese soft-shelled turtle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Siritapetawee, J. / Thammasirirak, S. / Yuvaniyama, J. / Robinson, R.C. | ||||||
Citation | Journal: to be published Title: Crystallization and the 1.9 angstroms of the egg-white lysozyme from a taiwanese soft-shelled turtle (trionyx sinensis wiegmann) Authors: Siritapetawee, J. / Thammasirirak, S. / Yuvaniyama, J. / Robinson, R.C. #1: Journal: Protein Sci. / Year: 1994 Title: Crystal structures of pheasant and guinea fowl egg-white lysozymes Authors: Lescar, J. / Souchon, H. / Alzari, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gv0.cif.gz | 35.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gv0.ent.gz | 27.4 KB | Display | PDB format |
PDBx/mmJSON format | 2gv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/2gv0 ftp://data.pdbj.org/pub/pdb/validation_reports/gv/2gv0 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14753.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: the correct name of the source is Trionyx sinensis wiegmann Source: (natural) Pelodiscus sinensis (Chinese soft-shelled turtle) References: UniProt: Q7LZQ1, lysozyme |
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#2: Chemical | ChemComp-SO4 / |
#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: 2.57 Å3/Da / Density % sol: 52.15 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R |
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Detector | Date: Mar 18, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→19.069 Å / Num. all: 12488 / Num. obs: 12433 / Limit h max: 19 / Limit h min: 0 / Limit k max: 29 / Limit k min: 0 / Limit l max: 38 / Limit l min: 0 |
Reflection scale | Group code: 1 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.046 / Mean I/σ(I) obs: 2.5 / Num. unique all: 12477 / % possible all: 99.4 |
-Phasing
Phasing MR | Rfactor: 0.451 / Cor.coef. Fo:Fc: 0.496 / Cor.coef. Io to Ic: 0.455
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→17.2 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.13 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.139 / 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: 21.154 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→17.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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