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Yorodumi- PDB-3lkf: LEUKOCIDIN F (HLGB) FROM STAPHYLOCOCCUS AUREUS WITH PHOSPHOCHOLIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lkf | ||||||
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Title | LEUKOCIDIN F (HLGB) FROM STAPHYLOCOCCUS AUREUS WITH PHOSPHOCHOLINE BOUND | ||||||
Components | LEUKOCIDIN F SUBUNIT | ||||||
Keywords | TOXIN / LEUKOTOXIN / HEMOLYSIN / PORE-FORMING TOXIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Olson, R. / Nariya, H. / Yokota, K. / Kamio, Y. / Gouaux, J.E. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Crystal structure of staphylococcal LukF delineates conformational changes accompanying formation of a transmembrane channel. Authors: Olson, R. / Nariya, H. / Yokota, K. / Kamio, Y. / Gouaux, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lkf.cif.gz | 76.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lkf.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 3lkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lkf_validation.pdf.gz | 375.7 KB | Display | wwPDB validaton report |
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Full document | 3lkf_full_validation.pdf.gz | 376.9 KB | Display | |
Data in XML | 3lkf_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 3lkf_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/3lkf ftp://data.pdbj.org/pub/pdb/validation_reports/lk/3lkf | 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: 34090.719 Da / Num. of mol.: 1 / Fragment: WATER-SOLUBLE MONOMER Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: SMITH 5R / Gene: LUKF / Plasmid: PTRCLUKF / Gene (production host): LUKF / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A / References: UniProt: P0A077 |
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#2: Chemical | ChemComp-PC / |
#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: 2.11 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9184 |
Detector | Type: ADSC / Detector: CCD / Date: Jun 1, 1998 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 26850 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.049 |
Reflection shell | Resolution: 1.8→1.86 Å / Rsym value: 0.176 / % possible all: 86 |
Reflection | *PLUS Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS % possible obs: 86 % / Rmerge(I) obs: 0.176 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PREVIOUSLY DETERMINED STRUCTURE Resolution: 1.9→6 Å / σ(F): 2
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Displacement parameters | Biso mean: 11.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 26815 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 11.017 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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