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Yorodumi- PDB-1qmd: calcium bound closed form alpha-toxin from Clostridium perfringens -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qmd | ||||||
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Title | calcium bound closed form alpha-toxin from Clostridium perfringens | ||||||
Components | PHOSPHOLIPASE C | ||||||
Keywords | HYDROLASE / ZINC PHOSPHOLIPASE C / GANGRENE DETERMINANT / C2 DOMAIN / CA AND MEMBRANE BINDING. | ||||||
Function / homology | Function and homology information calcium-dependent phospholipase C activity / phospholipase C / phosphatidylcholine phospholipase C activity / hemolysis in another organism / toxin activity / hydrolase activity / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM PERFRINGENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Naylor, C.E. / Miller, J. / Titball, R.W. / Basak, A.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Characterisation of the Calcium-Binding C-Terminal Domain of Clostridium Perfringens Alpha-Toxin Authors: Naylor, C.E. / Jepson, M. / Crane, D.T. / Titball, R.W. / Miller, J. / Basak, A.K. / Bolgiano, B. #1: Journal: Nat.Struct.Biol. / Year: 1998 Title: Structure of the Key Toxin in Gas-Gangrene Authors: Naylor, C.E. / Eaton, J.T. / Howells, A. / Justin, N. / Moss, D.S. / Titball, R.W. / Basak, A.K. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallisation and Preliminary X-Ray Diffraction Studies of Alpha-Toxin from Two Different Strains (Nctc-8237 and Cer89L43) of Clostridium Perfringens Authors: Basak, A.K. / Howells, A. / Eaton, J.T. / Moss, D.S. / Naylor, C. / Miller, J. / Titball, R.W. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qmd.cif.gz | 169.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qmd.ent.gz | 133.2 KB | Display | PDB format |
PDBx/mmJSON format | 1qmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qmd_validation.pdf.gz | 436.1 KB | Display | wwPDB validaton report |
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Full document | 1qmd_full_validation.pdf.gz | 442.3 KB | Display | |
Data in XML | 1qmd_validation.xml.gz | 30.3 KB | Display | |
Data in CIF | 1qmd_validation.cif.gz | 43.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/1qmd ftp://data.pdbj.org/pub/pdb/validation_reports/qm/1qmd | HTTPS FTP |
-Related structure data
Related structure data | 1qm6SC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99858, -0.05276, -0.00747), Vector: |
-Components
#1: Protein | Mass: 42577.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Strain: NCTC8237 / Plasmid: PUC18 / Cellular location (production host): PERIPLASMIC / Gene (production host): CPA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 References: UniProt: P15310, UniProt: Q0TV31*PLUS, phospholipase C #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Sequence details | 27 RESIDUES AT START OF SEQUENCE ARE A SIGNAL PEPTIDE NOT PRESENT IN MATURE, ACTIVE FOLDED PROTEIN. | |
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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: 2.45 Å3/Da / Density % sol: 50 % | ||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.7 Details: PROTEIN WAS CRYSTALLISED BY HANGING DROP FROM 1.8-2.0 M NACL IN 0.1 M NA ACETATE, PH 4.7 OR 4.8 | ||||||||||||||||||
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: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998 / Details: MIRRORS |
Radiation | Monochromator: GE(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 42803 / % possible obs: 97.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 6.5 / % possible all: 92.4 |
Reflection | *PLUS Num. measured all: 134096 |
Reflection shell | *PLUS % possible obs: 92.4 % / Num. unique obs: 5854 / Num. measured obs: 16154 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CALCIUM-FREE, CLOSED ALPHA-TOXIN PDB CODE: 1QM6 Resolution: 2.2→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 6850999.89 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: XPLOR AND REFMAC ALSO USED IN EARLIER STAGES OF REFINEMENT
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.2 Å2 / ksol: 0.375 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev position: 0.13 Å / Weight position: 200 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.183 / Rfactor Rfree: 0.257 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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