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Yorodumi- PDB-4bnk: Crystal structure of S. aureus FabI in complex with NADP and 5-fl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bnk | ||||||
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Title | Crystal structure of S. aureus FabI in complex with NADP and 5-fluoro- 2-phenoxyphenol | ||||||
Components | ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH] | ||||||
Keywords | OXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE SUPERFAMILY / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / SAFABI | ||||||
Function / homology | Function and homology information : / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding / identical protein binding Similarity search - Function | ||||||
Biological species | STAPHYLOCOCCUS AUREUS SUBSP. AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Schiebel, J. / Chang, A. / Bommineni, G.R. / Tonge, P.J. / Kisker, C. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Rational Optimization of Drug-Target Residence Time: Insights from Inhibitor Binding to the S. Aureus Fabi Enzyme-Product Complex. Authors: Chang, A. / Schiebel, J. / Yu, W. / Bommineni, G.R. / Pan, P. / Baxter, M.V. / Khanna, A. / Sotriffer, C.A. / Kisker, C.F. / Tonge, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bnk.cif.gz | 815.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bnk.ent.gz | 682.3 KB | Display | PDB format |
PDBx/mmJSON format | 4bnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bnk_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 4bnk_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 4bnk_validation.xml.gz | 87.5 KB | Display | |
Data in CIF | 4bnk_validation.cif.gz | 115.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/4bnk ftp://data.pdbj.org/pub/pdb/validation_reports/bn/4bnk | HTTPS FTP |
-Related structure data
Related structure data | 4bnfC 4bngC 4bnhC 4bniC 4bnjC 4bnlC 4bnmC 4bnnC 4alkS 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
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 31144.240 Da / Num. of mol.: 8 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS (bacteria) Strain: N315 / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7A6D8, UniProt: A0A0H3JLH9*PLUS, EC: 1.3.1.10 |
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-Non-polymers , 5 types, 810 molecules
#2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-FPL / #4: Chemical | ChemComp-GLU / #5: Chemical | ChemComp-CL / | #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: 2.94 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.1 M NA/K-PHOSPHATE PH 6.5, 36% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→46.11 Å / Num. obs: 94724 / % possible obs: 96.6 % / Observed criterion σ(I): 6 / Redundancy: 3.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ALK Resolution: 2.5→46.11 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.893 / SU B: 19.337 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.28 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.587 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→46.11 Å
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Refine LS restraints |
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