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Yorodumi- PDB-6dke: The X-ray crystal structure of Streptococcus pneumoniae Fatty Aci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dke | ||||||
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Title | The X-ray crystal structure of Streptococcus pneumoniae Fatty Acid Kinase (Fak) B1 protein loaded with palmitic acid (C16:0) to 1.76 Angstrom resolution | ||||||
Components | Fatty Acid Kinase (Fak) B1 protein | ||||||
Keywords | TRANSFERASE / Streptococcus pneumoniae / Fatty acid kinase / oleic acid | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Cuypers, M.G. / 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 Streptococcus pneumoniae Fatty Acid Kinase (Fak) B1 protein loaded with palmitic acid (C16:0) to 1.76 Angstrom resolution Authors: Cuypers, M.G. / 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 | 6dke.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dke.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 6dke.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dke_validation.pdf.gz | 601.3 KB | Display | wwPDB validaton report |
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Full document | 6dke_full_validation.pdf.gz | 601.7 KB | Display | |
Data in XML | 6dke_validation.xml.gz | 15 KB | Display | |
Data in CIF | 6dke_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/6dke ftp://data.pdbj.org/pub/pdb/validation_reports/dk/6dke | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar 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: 34538.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DP17 |
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#2: Chemical | ChemComp-PLM / |
#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: 2.12 Å3/Da / Density % sol: 42.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES pH6.5, 30% (w/v) PEG4000 / Temp details: controlled temperature room |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→62.34 Å / Num. obs: 28063 / % possible obs: 97.9 % / Redundancy: 2.7 % / Biso Wilson estimate: 22 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.042 / Rrim(I) all: 0.072 / Χ2: 0.88 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.76→1.79 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2 / Num. unique obs: 1592 / CC1/2: 0.746 / Rpim(I) all: 0.355 / Rrim(I) all: 0.613 / Χ2: 0.89 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→46.574 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→46.574 Å
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Refine LS restraints |
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LS refinement shell |
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