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Yorodumi- PDB-1qxm: Crystal structure of a hemagglutinin component (HA1) from type C ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qxm | ||||||
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Title | Crystal structure of a hemagglutinin component (HA1) from type C Clostridium botulinum | ||||||
Components | HA1 | ||||||
Keywords | TOXIN / Clostridium botulinum / hemagglutinin / HA1 / trefoil | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium botulinum D phage (virus) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 1.7 Å | ||||||
Authors | Inoue, K. / Sobhany, M. / Transue, T.R. / Oguma, K. / Pedersen, L.C. / Negishi, M. | ||||||
Citation | Journal: Microbiology / Year: 2003 Title: Structural analysis by X-ray crystallography and calorimetry of a haemagglutinin component (HA1) of the progenitor toxin from Clostridium botulinum. Authors: Inoue, K. / Sobhany, M. / Transue, T.R. / Oguma, K. / Pedersen, L.C. / Negishi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qxm.cif.gz | 142.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qxm.ent.gz | 111.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qxm_validation.pdf.gz | 446.8 KB | Display | wwPDB validaton report |
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Full document | 1qxm_full_validation.pdf.gz | 452.8 KB | Display | |
Data in XML | 1qxm_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 1qxm_validation.cif.gz | 44.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/1qxm ftp://data.pdbj.org/pub/pdb/validation_reports/qx/1qxm | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | not known |
-Components
#1: Protein | Mass: 35549.348 Da / Num. of mol.: 2 / Fragment: hemagglutinin component HA1 / Mutation: type C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum D phage (virus) / Species: Clostridium phage c-st / Plasmid: pGEX-4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P46084, UniProt: P0DPR1*PLUS #2: Chemical | ChemComp-EDO / #3: 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: 2.41 Å3/Da / Density % sol: 49.03 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: sirsas / pH: 5.5 Details: MES, PEG8000, MgCl2, pH 5.5, SIRSAS, temperature 296K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→25 Å / Num. all: 71843 / Num. obs: 71843 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 15.7 Å2 / Rsym value: 0.042 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2 % / Mean I/σ(I) obs: 8 / Num. unique all: 6546 / Rsym value: 0.15 / % possible all: 87.6 |
Reflection | *PLUS Num. measured all: 203352 / Rmerge(I) obs: 0.042 |
Reflection shell | *PLUS % possible obs: 87.6 % / Rmerge(I) obs: 0.15 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.7→24.58 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.5967 Å2 / ksol: 0.361759 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.2 Å2
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Refine analyze | Luzzati coordinate error free: 0.2 Å / Luzzati sigma a free: 0.11 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→24.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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