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Yorodumi- PDB-1gir: CRYSTAL STRUCTURE OF THE ENZYMATIC COMPONET OF IOTA-TOXIN FROM CL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gir | ||||||
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Title | CRYSTAL STRUCTURE OF THE ENZYMATIC COMPONET OF IOTA-TOXIN FROM CLOSTRIDIUM PERFRINGENS WITH NADPH | ||||||
Components | IOTA TOXIN COMPONENT IA | ||||||
Keywords | TOXIN / enzymatic component | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium perfringens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å | ||||||
Authors | Tsuge, H. / Nagahama, M. / Nishimura, H. / Hisatsune, J. / Sakaguchi, Y. / Itogawa, Y. / Katunuma, N. / Sakurai, J. | ||||||
Citation | Journal: J.MOL.BIOL. / Year: 2003 Title: Crystal Structure and Site-directed Mutagenesis of Enzymatic Components from Clostridium perfringens Iota-toxin Authors: Tsuge, H. / Nagahama, M. / Nishimura, H. / Hisatsune, J. / Sakaguchi, Y. / Itogawa, Y. / Katunuma, N. / Sakurai, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gir.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gir.ent.gz | 76 KB | Display | PDB format |
PDBx/mmJSON format | 1gir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gir_validation.pdf.gz | 471.3 KB | Display | wwPDB validaton report |
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Full document | 1gir_full_validation.pdf.gz | 483.3 KB | Display | |
Data in XML | 1gir_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 1gir_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/1gir ftp://data.pdbj.org/pub/pdb/validation_reports/gi/1gir | HTTPS FTP |
-Related 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: 47648.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Clostridium perfringens (bacteria) / References: UniProt: Q46220 |
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#2: Chemical | ChemComp-NDP / |
#3: Water | ChemComp-HOH / |
-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: 52.37 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Details: PEG4000, NADPH, temperature 277.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 |
Detector | Type: ADSC QUANTUM / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 26770 / Num. obs: 26770 / % possible obs: 91.2 % / Redundancy: 1.4 % / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.297 / % possible all: 78.6 |
Reflection | *PLUS Highest resolution: 2.1 Å |
Reflection shell | *PLUS Highest resolution: 2.1 Å / % possible obs: 78.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.1→14.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 370484.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.7813 Å2 / ksol: 0.352911 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→14.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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