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Yorodumi- PDB-4fs3: Crystal structure of Staphylococcus aureus enoyl-ACP reductase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fs3 | ||||||
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Title | Crystal structure of Staphylococcus aureus enoyl-ACP reductase in complex with NADP and AFN-1252 | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADPH] FabI | ||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold / short chain dehydrogenase / NADPH binding | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / : / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NADP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kaplan, N. / Yethon, J. / Bardouniotis, E. / Thalakada, R. / Albert, M. / Awrey, D.E. / Romanov, V. / Dorsey, M. / Ramnauth, J. / Clarke, T.E. ...Kaplan, N. / Yethon, J. / Bardouniotis, E. / Thalakada, R. / Albert, M. / Awrey, D.E. / Romanov, V. / Dorsey, M. / Ramnauth, J. / Clarke, T.E. / Schmid, M.B. / Berman, J. / Pauls, H.W. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2012 Title: Mode of Action, In Vitro Activity, and In Vivo Efficacy of AFN-1252, a Selective Antistaphylococcal FabI Inhibitor. Authors: Kaplan, N. / Albert, M. / Awrey, D. / Bardouniotis, E. / Berman, J. / Clarke, T. / Dorsey, M. / Hafkin, B. / Ramnauth, J. / Romanov, V. / Schmid, M.B. / Thalakada, R. / Yethon, J. / Pauls, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fs3.cif.gz | 72 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fs3.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 4fs3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/4fs3 ftp://data.pdbj.org/pub/pdb/validation_reports/fs/4fs3 | HTTPS FTP |
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-Related structure data
Related structure data | 1mfpS 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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-Components
#1: Protein | Mass: 28024.900 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: MRSA252 / Gene: fabI, SAR0978 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GI75, EC: 1.3.1.10 |
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#2: Chemical | ChemComp-0WD / [[( |
#3: Chemical | ChemComp-0WE / |
#4: 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: 2.88 Å3/Da / Density % sol: 57.25 % |
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Crystal grow | Temperature: 298 K / pH: 7.4 Details: 32% (w/v) PEG400, 0.1 M NaHEPES, 0.2 M calcium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 16, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 30598 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Rsym value: 0.096 / Net I/σ(I): 38.8 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.529 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MFP Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.001 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.106 / 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: 22.665 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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