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Yorodumi- PDB-2z6j: Crystal Structure of S. pneumoniae Enoyl-Acyl Carrier Protein Red... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z6j | ||||||
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Title | Crystal Structure of S. pneumoniae Enoyl-Acyl Carrier Protein Reductase (FabK) in Complex with an Inhibitor | ||||||
Components | Trans-2-enoyl-ACP reductase II | ||||||
Keywords | OXIDOREDUCTASE / FATTY ACID SYNTHESIS / ANTIBIOTICS / FLAVOPROTEIN | ||||||
Function / homology | Function and homology information nitronate monooxygenase / Oxidoreductases; Acting on the CH-CH group of donors / nitronate monooxygenase activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Saito, J. / Yamada, M. / Watanabe, T. / Takeuchi, Y. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Crystal structure of enoyl-acyl carrier protein reductase (FabK) from Streptococcus pneumoniae reveals the binding mode of an inhibitor. Authors: Saito, J. / Yamada, M. / Watanabe, T. / Iida, M. / Kitagawa, H. / Takahata, S. / Ozawa, T. / Takeuchi, Y. / Ohsawa, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z6j.cif.gz | 128.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z6j.ent.gz | 98.7 KB | Display | PDB format |
PDBx/mmJSON format | 2z6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z6j_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2z6j_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2z6j_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 2z6j_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/2z6j ftp://data.pdbj.org/pub/pdb/validation_reports/z6/2z6j | HTTPS FTP |
-Related structure data
Related structure data | 2z6iSC S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35289.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Plasmid: pET-21b(+) / Production host: Escherichia coli (E. coli) References: UniProt: Q9FBC5, enoyl-[acyl-carrier-protein] reductase (NADH) |
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-Non-polymers , 5 types, 81 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MPD / ( | #6: Water | ChemComp-HOH / | |
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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: 2.25 Å3/Da / Density % sol: 45.35 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 8-15% PEG 1000, 8-15% MPD, 0.1M MES pH 5.5-7.0, 0.1M ammonium chloride, 0.2M calcium chloride, 5mM dithiothreitol , VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 16, 2005 Details: A fixed exit Si double crystal monochromator followed byStandard double crystal monochromator and Rh-coated downward-deflection mirror with a typical glancing angle of 3.7 mrad. |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29.08 Å / Num. obs: 25448 / % possible obs: 91.9 % / Redundancy: 3 % / Biso Wilson estimate: 27.024 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 4.5 / % possible all: 90 |
-Processing
Software |
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Refinement | Starting model: 2Z6I Resolution: 2.3→29.08 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.859 / SU B: 9.273 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.568 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: AUTHOR skipped the molecular replacement and directly proceeded to rigid body refinement using the model. 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.443 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→29.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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