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Yorodumi- PDB-2vk5: THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vk5 | ||||||
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Title | THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES | ||||||
Components | EXO-ALPHA-SIALIDASE | ||||||
Keywords | HYDROLASE / SIALIDASE / GLYCOSIDASE / SIALIC ACID / CLOSTRIDIUM PERFRINGENS | ||||||
Function / homology | Function and homology information : / : / : / exo-alpha-sialidase / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM PERFRINGENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å | ||||||
Authors | Newstead, S.L. / Potter, J.A. / Wilson, J.C. / Xu, G. / Chien, C.H. / Watts, A.G. / Withers, S.G. / Taylor, G.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: The Structure of Clostridium Perfringens Nani Sialidase and its Catalytic Intermediates. Authors: Newstead, S.L. / Potter, J.A. / Wilson, J.C. / Xu, G. / Chien, C.H. / Watts, A.G. / Withers, S.G. / Taylor, G.L. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vk5.cif.gz | 236.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vk5.ent.gz | 183.9 KB | Display | PDB format |
PDBx/mmJSON format | 2vk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vk5_validation.pdf.gz | 440 KB | Display | wwPDB validaton report |
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Full document | 2vk5_full_validation.pdf.gz | 447.7 KB | Display | |
Data in XML | 2vk5_validation.xml.gz | 30.3 KB | Display | |
Data in CIF | 2vk5_validation.cif.gz | 50.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/2vk5 ftp://data.pdbj.org/pub/pdb/validation_reports/vk/2vk5 | HTTPS FTP |
-Related structure data
Related structure data | 2bf6C 2vk6C 2vk7C 1sllS 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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Unit cell |
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-Components
#1: Protein | Mass: 50405.852 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 243-694 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q59310, exo-alpha-sialidase | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 34 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 0.97→20 Å / Num. obs: 281317 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 0.97→1.02 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.6 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SLL Resolution: 0.97→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 0.97→20 Å
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Refine LS restraints |
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