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Yorodumi- PDB-4cv2: Crystal structure of E. coli FabI in complex with NADH and CG400549 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cv2 | ||||||
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Title | Crystal structure of E. coli FabI in complex with NADH and CG400549 | ||||||
Components | ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] | ||||||
Keywords | OXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE SUPERFAMILY / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / ECFABI | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / biotin biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Tareilus, M. / Schiebel, J. / Chang, A. / Shah, S. / Tonge, P.J. / Kisker, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Rational Design of Broad Spectrum Antibacterial Activity Based on a Clinically Relevant Enoyl-Acyl Carrier Protein (Acp) Reductase Inhibitor. Authors: Schiebel, J. / Chang, A. / Shah, S. / Lu, Y. / Liu, L. / Pan, P. / Hirschbeck, M.W. / Tareilus, M. / Eltschkner, S. / Yu, W. / Cummings, J.E. / Knudson, S.E. / Bommineni, G.R. / Walker, S.G. ...Authors: Schiebel, J. / Chang, A. / Shah, S. / Lu, Y. / Liu, L. / Pan, P. / Hirschbeck, M.W. / Tareilus, M. / Eltschkner, S. / Yu, W. / Cummings, J.E. / Knudson, S.E. / Bommineni, G.R. / Walker, S.G. / Slayden, R.A. / Sotriffer, C.A. / Tonge, P.J. / Kisker, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cv2.cif.gz | 199.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cv2.ent.gz | 161 KB | Display | PDB format |
PDBx/mmJSON format | 4cv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cv2_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4cv2_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4cv2_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 4cv2_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/4cv2 ftp://data.pdbj.org/pub/pdb/validation_reports/cv/4cv2 | HTTPS FTP |
-Related structure data
Related structure data | 4bkuC 4cuzC 4cv0C 4cv1C 4cv3C 1qsgS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28964.068 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: C6EFU4, UniProt: A0A140NA83*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | #3: Chemical | #4: 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: 2.56 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | pH: 10.5 / Details: 0.2 M NH4AC, 0.1 M CAPS PH 10.5, 20% PEG 8000 |
-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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.1 Å / Num. obs: 56987 / % possible obs: 98.7 % / Observed criterion σ(I): 6 / Redundancy: 14.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2.3 / % possible all: 96.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QSG Resolution: 1.8→69.38 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.391 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DUE TO VERY WEAK ELECTRON DENSITY, THE LOOP REGION 193-210 WAS NOT MODELED
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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: 33.009 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→69.38 Å
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Refine LS restraints |
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