+Open data
-Basic information
Entry | Database: PDB / ID: 3gne | ||||||
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Title | Crystal structure of alginate lyase vAL-1 from Chlorella virus | ||||||
Components | VAL-1 | ||||||
Keywords | LYASE / alginate lyase / polysaccharide lyase family 14 / chlorella virus | ||||||
Function / homology | : / Polysaccharide lyase 14 / Jelly Rolls - #200 / Jelly Rolls / Sandwich / Mainly Beta / CITRATE ANION / VAL-1 Function and homology information | ||||||
Biological species | Chlorella virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å | ||||||
Authors | Ogura, K. / Yamasaki, M. / Hashidume, T. / Yamada, T. / Mikami, B. / Hashimoto, W. / Murata, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Crystal structure of family 14 polysaccharide lyase with pH-dependent modes of action Authors: Ogura, K. / Yamasaki, M. / Yamada, T. / Mikami, B. / Hashimoto, W. / Murata, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gne.cif.gz | 240.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gne.ent.gz | 194.3 KB | Display | PDB format |
PDBx/mmJSON format | 3gne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gne_validation.pdf.gz | 460.2 KB | Display | wwPDB validaton report |
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Full document | 3gne_full_validation.pdf.gz | 468.2 KB | Display | |
Data in XML | 3gne_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 3gne_validation.cif.gz | 45.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/3gne ftp://data.pdbj.org/pub/pdb/validation_reports/gn/3gne | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28042.572 Da / Num. of mol.: 2 / Fragment: C-terminal domain, residues 106-349 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorella virus / Strain: CVK-2 / Gene: vAL-1 / Plasmid: pET21b (Novagen) / Production host: Escherichia coli (E. coli) References: UniProt: Q9DTZ2, mannuronate-specific alginate lyase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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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: 2.19 Å3/Da / Density % sol: 43.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 15% PEG 4000, 15% iso-Propanol, 0.1M sodium citrate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.7 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 12, 2008 |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 142201 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Num. measured all: 747443 |
Reflection shell | Resolution: 1.2→1.24 Å |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.2→10 Å / Num. parameters: 43086 / Num. restraintsaints: 53335 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 24 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4638 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints |
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