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Yorodumi- PDB-7rm7: The X-ray crystal structure of the N-terminal domain of Staphyloc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rm7 | ||||||
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Title | The X-ray crystal structure of the N-terminal domain of Staphylococcus aureus Fatty Acid Kinase A (FakA, residues 1-208) in complex with ADP to 1.025 Angstrom resolution | ||||||
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: 1.025 Å | ||||||
Authors | Cuypers, M.G. / Subramanian, C. / Rock, C.O. / White, S.W. | ||||||
Citation | Journal: To Be Published Title: The X-ray crystal structure of the N-terminal domain of Staphylococcus aureus Fatty Acid Kinase A (FakA, residues 1-208) in complex with ADP to 1.025 Angstrom resolution 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 | 7rm7.cif.gz | 193.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rm7.ent.gz | 148.6 KB | Display | PDB format |
PDBx/mmJSON format | 7rm7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/7rm7 ftp://data.pdbj.org/pub/pdb/validation_reports/rm/7rm7 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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-GOL / | ||||
#3: Chemical | ChemComp-ADP / | ||||
#4: Chemical | ChemComp-MG / #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: 2.03 Å3/Da / Density % sol: 39.51 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2M MgCl2, 0.1M Tris Hcl pH8.5, 30%PEG4000 (JCSG core IV #21) |
-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 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.025→34.24 Å / Num. obs: 95789 / % possible obs: 95.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 8.3 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.02 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.025→1.04 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 3447 / CC1/2: 0.65 / Rpim(I) all: 0.396 / % possible all: 70.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.025→34.24 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.911 / SU ML: 0.02 / Cross valid method: FREE R-VALUE / ESU R: 0.022 / ESU R Free: 0.024 Details: Phasing was performed using this data set as a remote wavelength coupled with the SAD data from a cobalt-derivatized crystal (PDB ID 7RZK). Hydrogens have been used if present in the input file
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.035 Å2
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Refinement step | Cycle: LAST / Resolution: 1.025→34.24 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 14.9801 Å / Origin y: 5.2362 Å / Origin z: -12.5135 Å
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Refinement TLS group | Selection: ALL |