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Yorodumi- PDB-4q7g: 1.7 Angstrom Crystal Structure of leukotoxin LukD from Staphyloco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q7g | ||||||
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Title | 1.7 Angstrom Crystal Structure of leukotoxin LukD from Staphylococcus aureus. | ||||||
Components | Leucotoxin LukDv | ||||||
Keywords | TOXIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / Leukocidin-like / Distorted Sandwich / Leukocidin | ||||||
Function / homology | Function and homology information hemolysis in another organism / cytolysis in another organism / : / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Minasov, G. / Nocadello, S. / Shuvalova, L. / Shatsman, S. / Kwon, K. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: Crystal structures of the components of the Staphylococcus aureus leukotoxin ED. Authors: Nocadello, S. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Sabini, E. / Bagnoli, F. / Grandi, G. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q7g.cif.gz | 150.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q7g.ent.gz | 119.2 KB | Display | PDB format |
PDBx/mmJSON format | 4q7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/4q7g ftp://data.pdbj.org/pub/pdb/validation_reports/q7/4q7g | HTTPS FTP |
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-Related structure data
Related structure data | 3rohC 1pvlS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36873.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: COL / Gene: hlgB, lukD, lukDv, SAS1748 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): KRXpGro7 / References: UniProt: Q6G8A9, UniProt: A0A0H2WX25*PLUS |
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#2: Chemical | ChemComp-BTB / |
#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: 2.28 Å3/Da / Density % sol: 46.02 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein: 2.6mG/mL, 0.5M Sodium chloride, 0.01M Tris-HCL buffer, 0.5mM TCEP; Screen: Classics II (G7), 0.2M Ammonium acetate, 0.1M BIS-TRIS, 25% (w/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, ...Details: Protein: 2.6mG/mL, 0.5M Sodium chloride, 0.01M Tris-HCL buffer, 0.5mM TCEP; Screen: Classics II (G7), 0.2M Ammonium acetate, 0.1M BIS-TRIS, 25% (w/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 10, 2014 / Details: beryllium lenses |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 37802 / Num. obs: 37802 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 3 / Num. unique all: 1897 / Rsym value: 0.615 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1PVL Resolution: 1.7→27.95 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.988 / SU ML: 0.068 Isotropic thermal model: Thermal Factors Individually Isotropically Refined Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→27.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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