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Yorodumi- PDB-7pps: apo FabB from Pseudomonas aeruginosa with single point mutation C161A -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pps | ||||||
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Title | apo FabB from Pseudomonas aeruginosa with single point mutation C161A | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | ||||||
Keywords | TRANSFERASE / Fatty acid biosynthesis pathway / FabB | ||||||
Function / homology | Function and homology information beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PA14 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Georgiou, C. / Brenk, R. / Yadrykhinsky, V. | ||||||
Funding support | Norway, 1items
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Citation | Journal: F1000Res / Year: 2021 Title: Crystal structure of Pseudomonas aeruginosa FabB C161A, a template for structure-based design for new antibiotics. Authors: Yadrykhins'ky, V. / Georgiou, C. / Brenk, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pps.cif.gz | 333.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pps.ent.gz | 270.8 KB | Display | PDB format |
PDBx/mmJSON format | 7pps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/7pps ftp://data.pdbj.org/pub/pdb/validation_reports/pp/7pps | HTTPS FTP |
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-Related structure data
Related structure data | 4xoxS 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 1 - 404 / Label seq-ID: 3 - 406
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-Components
#1: Protein | Mass: 43085.531 Da / Num. of mol.: 2 / Mutation: C161A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Gene: fabB, PA14_43690 / Production host: Escherichia coli (E. coli) References: UniProt: Q02K94, beta-ketoacyl-[acyl-carrier-protein] synthase I #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-IOD / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.09 Å3/Da / Density % sol: 41.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG3350, 20% Ethylene glycol, 0.2M NaI, 0.1M Bis-Tris propane pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.976246 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976246 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→47.19 Å / Num. obs: 174480 / % possible obs: 99.7 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 8364 / CC1/2: 0.928 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4xox Resolution: 1.3→47.19 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.016 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.389 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→47.19 Å
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Refine LS restraints |
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