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Yorodumi- PDB-6nyu: The X-ray crystal structure of Staphylococcus aureus Fatty Acid K... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nyu | ||||||
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Title | The X-ray crystal structure of Staphylococcus aureus Fatty Acid Kinase (Fak) B1 F263T mutant protein to 2.18 Angstrom resolution | ||||||
Components | DegV domain-containing protein | ||||||
Keywords | TRANSFERASE / Fatty acid kinase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.183 Å | ||||||
Authors | Cuypers, M.G. / Gullett, J.M. / Subramanian, C. / White, S.W. / Rock, C.O. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: The X-ray crystal structure of STAPHYLOCOCCUS AUREUS Fatty Acid Kinase (Fak) B1 protein F263T mutant to 2.18 Angstrom resolution Authors: Cuypers, M.G. / Gullett, J.M. / Subramanian, C. / White, S.W. / Rock, C.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nyu.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nyu.ent.gz | 100.3 KB | Display | PDB format |
PDBx/mmJSON format | 6nyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nyu_validation.pdf.gz | 984.4 KB | Display | wwPDB validaton report |
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Full document | 6nyu_full_validation.pdf.gz | 991.1 KB | Display | |
Data in XML | 6nyu_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 6nyu_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/6nyu ftp://data.pdbj.org/pub/pdb/validation_reports/ny/6nyu | HTTPS FTP |
-Related structure data
Related structure data | 5utoS S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 32055.436 Da / Num. of mol.: 2 / Mutation: F263T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: BTN44_08795, CV021_09110, EP54_02745, EQ90_03735, ERS072840_01626, HMPREF3211_01094, NCTC10654_00855, NCTC11940_00723, NCTC13131_00828, NCTC13196_00435, NCTC6133_00899, NCTC7878_03402, SAMEA1531701_00562 Production host: Escherichia coli (E. coli) / References: UniProt: X5EH37, UniProt: P0A0N2*PLUS #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.13 Å3/Da / Density % sol: 42.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: PH 6.5 0.1M MES/IMIDAZOLE, 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 0.03M NANO3, 0.03M NA2HPO4, 0.03M (NH4)2 SO4 Temp details: controlled room |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryostream - post 88K flash freezing / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→80.56 Å / Num. obs: 26506 / % possible obs: 96.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.5 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.08 / Rrim(I) all: 0.156 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.18→2.25 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1800 / CC1/2: 0.552 / Rpim(I) all: 0.379 / Rrim(I) all: 0.548 / % possible all: 76.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UTO Resolution: 2.183→40.279 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.81
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.183→40.279 Å
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Refine LS restraints |
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LS refinement shell |
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