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Yorodumi- PDB-3im0: Crystal structure of Chlorella virus vAL-1 soaked in 200mM D-gluc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3im0 | ||||||
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Title | Crystal structure of Chlorella virus vAL-1 soaked in 200mM D-glucuronic acid, 10% PEG-3350, and 200mM glycine-NaOH (pH 10.0) | ||||||
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 / beta-D-glucopyranuronic acid / VAL-1 Function and homology information | ||||||
Biological species | Chlorella virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.66 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 | 3im0.cif.gz | 74.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3im0.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 3im0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3im0_validation.pdf.gz | 446.1 KB | Display | wwPDB validaton report |
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Full document | 3im0_full_validation.pdf.gz | 452.3 KB | Display | |
Data in XML | 3im0_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 3im0_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/3im0 ftp://data.pdbj.org/pub/pdb/validation_reports/im/3im0 | HTTPS FTP |
-Related structure data
Related structure data | 3a0nC 3gneSC S: Starting model for refinement C: citing same article (ref.) |
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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: 28042.572 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 106-349 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorella virus / Strain: CVK-2 / Gene: vAL-1 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9DTZ2, mannuronate-specific alginate lyase |
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#2: Sugar | ChemComp-BDP / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | SINCE O1 OF BDP IS MISSING IN THIS ENTRY, ALTERNATIV |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 12% PEG 3350, 0.2M ammonium formate, 0.1M hepes-NaOH pH7.0, 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: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 29, 2009 |
Radiation | Monochromator: Fixed exit Si 111 double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→26.32 Å / Num. all: 34464 / Num. obs: 34464 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 74.6 |
Reflection shell | Resolution: 1.66→1.72 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 16.5 / Num. unique all: 3330 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: PDB ENTRY 3GNE Resolution: 1.66→10 Å / Num. parameters: 9879 / Num. restraintsaints: 8643 / Isotropic thermal model: Isotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 14 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2363.52 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→10 Å
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Refine LS restraints |
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