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- PDB-1qm6: Closed form of Clostridium perfringens alpha-toxin strain NCTC8237 -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qm6 | ||||||
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Title | Closed form of Clostridium perfringens alpha-toxin strain NCTC8237 | ||||||
![]() | PHOSPHOLIPASE C | ||||||
![]() | HYDROLASE / ZINC PHOSPHOLIPASE C / GANGRENE DETERMINANT / C2 DOMAIN / CA AND MEMBRANE BINDING. | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Naylor, C.E. / Miller, J. / Titball, R.W. / Basak, A.K. | ||||||
![]() | ![]() 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: ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.8 KB | Display | ![]() |
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PDB format | ![]() | 126.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.8 KB | Display | ![]() |
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Full document | ![]() | 442.8 KB | Display | |
Data in XML | ![]() | 27.2 KB | Display | |
Data in CIF | ![]() | 37.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qmdC ![]() 1ca1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: (0.99865, -0.05189, -0.00206), Vector: |
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Components
#1: Protein | Mass: 42577.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P15310, UniProt: Q0TV31*PLUS, phospholipase C #2: Chemical | ChemComp-ZN / #3: 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: ![]() |
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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: ![]() ![]() ![]() |
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: 2.6→30 Å / Num. obs: 29145 / % possible obs: 90.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 4.2 / % possible all: 87.9 |
Reflection | *PLUS Num. measured all: 98122 |
Reflection shell | *PLUS % possible obs: 87.9 % / Num. unique obs: 3939 / Num. measured obs: 14192 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: CALCIUM-FREE, CLOSED ALPHA-TOXIN STRAIN CER89L43 (PDB CODE: 1CA1) Resolution: 2.5→30 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL (ANISOTROPIC) / Bsol: 10 Å2 / ksol: 0.406 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev Biso : 1.95 Å2 / Rms dev position: 0.031 Å / Weight Biso : 2 / Weight position: 300 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.6 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.22 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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