[English] 日本語
Yorodumi- PDB-3gxr: The crystal structure of g-type lysozyme from Atlantic cod (Gadus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gxr | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
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. Structure with NAG to 1.7 | |||||||||
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: 1.7 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3gxr.cif.gz | 160.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3gxr.ent.gz | 128.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gxr_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3gxr_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 3gxr_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 3gxr_validation.cif.gz | 46.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/3gxr ftp://data.pdbj.org/pub/pdb/validation_reports/gx/3gxr | HTTPS FTP |
-Related structure data
Related structure data | 3gxkSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-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: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | #4: Water | ChemComp-HOH / | Sequence details | THE DISCREPANC | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.97 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 29, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→34 Å / Num. all: 70454 / Num. obs: 69961 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 22.34 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.353 / % possible all: 95.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GXK Resolution: 1.7→34 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.719 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 21.496 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→34 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
|