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Yorodumi- PDB-3gxk: The crystal structure of g-type lysozyme from Atlantic cod (Gadus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gxk | ||||||
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Title | The crystal structure of g-type lysozyme from Atlantic cod (Gadus morhua L.) in complex with NAG oligomers sheds new light on substrate binding and the catalytic mechanism. Native structure to 1.9 | ||||||
Components | Goose-type lysozyme 1 | ||||||
Keywords | HYDROLASE / Atlantic cod / fish lysozyme / active site residues / substrate binding sites / surface potential / muramidase activity / immune system | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Gadus morhua (Atlantic cod) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Helland, R. / Larsen, R.L. / Finstad, S. / Kyomuhendo, P. / Larsen, A.N. | ||||||
Citation | Journal: Cell.Mol.Life Sci. / Year: 2009 Title: Crystal structures of g-type lysozyme from Atlantic cod shed new light on substrate binding and the catalytic mechanism. Authors: Helland, R. / Larsen, R.L. / Finstad, S. / Kyomuhendo, P. / Larsen, A.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gxk.cif.gz | 154 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gxk.ent.gz | 123.2 KB | Display | PDB format |
PDBx/mmJSON format | 3gxk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/3gxk ftp://data.pdbj.org/pub/pdb/validation_reports/gx/3gxk | HTTPS FTP |
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-Related structure data
Related structure data | 3gxrC 154lS 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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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20831.008 Da / Num. of mol.: 4 / Fragment: UNP residues 31-217 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gadus morhua (Atlantic cod) / Gene: lysozyme / Plasmid: pET151/D-TOPO gLYS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: B9TU22, lysozyme #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE DISCREPANC | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 48-53% ammonium sulphate, 5mM CoCl2, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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 | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.02 Å / Num. all: 50454 / Num. obs: 50202 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 18.99 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 3.3 / Num. unique all: 7068 / Rsym value: 0.221 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 154L Resolution: 1.9→48.02 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.896 / SU B: 3.827 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.173 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.764 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→48.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 Å / Total num. of bins used: 20
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