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Yorodumi- PDB-3gns: Crystal Structure of the Staphylococcus aureus Enoyl-Acyl Carrier... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gns | ||||||
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Title | Crystal Structure of the Staphylococcus aureus Enoyl-Acyl Carrier Protein Reductase (FabI) in apo form (one molecule in AU) | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / Enoyl reductase | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NADP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.706 Å | ||||||
Authors | Priyadarshi, A. / Hwang, K.Y. | ||||||
Citation | Journal: Proteins / Year: 2010 Title: Structural insights into Staphylococcus aureus enoyl-ACP reductase (FabI), in complex with NADP and triclosan Authors: Priyadarshi, A. / Kim, E.E. / Hwang, K.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gns.cif.gz | 58.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gns.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gns_validation.pdf.gz | 430 KB | Display | wwPDB validaton report |
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Full document | 3gns_full_validation.pdf.gz | 466.5 KB | Display | |
Data in XML | 3gns_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 3gns_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/3gns ftp://data.pdbj.org/pub/pdb/validation_reports/gn/3gns | HTTPS FTP |
-Related structure data
Related structure data | 3gntC 3gr6C 2pd3S C: citing same article (ref.) 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: 28351.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: fabI / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q6GI75, enoyl-[acyl-carrier-protein] reductase (NADH) |
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#2: Chemical | ChemComp-NA / |
#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: 2.58 Å3/Da / Density % sol: 52.39 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 10~15% PEG 400, 0.1M Tris pH 8.3~8.5, 4% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 8, 2008 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 7634 / Num. obs: 7261 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.28 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 2.95 / Num. unique all: 451 / Rsym value: 0.28 / % possible all: 56 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PD3 Resolution: 2.706→37.66 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.868 / SU B: 17.01 / SU ML: 0.332 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.191 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.514 Å2
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Refine analyze | Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.706→37.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.706→2.775 Å / Total num. of bins used: 20
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