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Yorodumi- PDB-7rzk: Co-soak crystal structure of the N-terminal domain of Staphylococ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rzk | ||||||
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Title | Co-soak crystal structure of the N-terminal domain of Staphylococcus aureus Fatty Acid Kinase A (FakA, residues 1-208) in complex with ADP to 1.9 Angstrom resolution - SAD data | ||||||
Components | Fatty Acid Kinase A | ||||||
Keywords | LIGASE / Fatty acid kinase A / phosphorylation / fatty acid / N-terminus domain | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Cuypers, M.G. / Subramanian, C. / Rock, C.O. / White, S.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Co-soak crystal structure of the N-terminal domain of Staphylococcus aureus Fatty Acid Kinase A (FakA, residues 1-208) in complex with ADP to 1.9 Angstrom resolution - SAD data Authors: Cuypers, M.G. / Subramanian, C. / Rock, C.O. / White, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rzk.cif.gz | 68.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rzk.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 7rzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/7rzk ftp://data.pdbj.org/pub/pdb/validation_reports/rz/7rzk | HTTPS FTP |
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-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: 24445.777 Da / Num. of mol.: 1 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7A5Z4 | ||||||
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#2: Chemical | ChemComp-ADP / | ||||||
#3: Chemical | #4: Chemical | ChemComp-CO / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M ammonium formate, 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.6039 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.6039 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→81.25 Å / Num. obs: 16525 / % possible obs: 100 % / Redundancy: 11.7 % / Biso Wilson estimate: 19.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.033 / Χ2: 0.55 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.868 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1041 / CC1/2: 0.883 / Rpim(I) all: 0.336 / Χ2: 0.51 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→46.95 Å / SU ML: 0.1793 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 19.5048 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→46.95 Å
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Refine LS restraints |
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LS refinement shell |
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