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Yorodumi- PDB-4cv1: Crystal structure of S. aureus FabI in complex with NADPH and CG400549 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cv1 | ||||||
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Title | Crystal structure of S. aureus FabI in complex with NADPH and CG400549 | ||||||
Components | ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] | ||||||
Keywords | OXIDOREDUCTASE / ENOYL-ACP REDUCTASE / 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 | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | 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 | 4cv1.cif.gz | 833.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cv1.ent.gz | 699.7 KB | Display | PDB format |
PDBx/mmJSON format | 4cv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cv1_validation.pdf.gz | 4.9 MB | Display | wwPDB validaton report |
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Full document | 4cv1_full_validation.pdf.gz | 4.8 MB | Display | |
Data in XML | 4cv1_validation.xml.gz | 87.1 KB | Display | |
Data in CIF | 4cv1_validation.cif.gz | 116.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/4cv1 ftp://data.pdbj.org/pub/pdb/validation_reports/cv/4cv1 | HTTPS FTP |
-Related structure data
Related structure data | 4bkuC 4cuzC 4cv0C 4cv2C 4cv3C 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.) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / 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 , 6 types, 878 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NDP / #4: Chemical | ChemComp-PT6 / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-CL / | #7: 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 Å3/Da / Density % sol: 38.62 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 0.2 M LI2SO4, 24% PEG 3350, pH 8.0 |
-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: Sep 13, 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: 1.95→47.56 Å / Num. obs: 146661 / % possible obs: 100 % / Observed criterion σ(I): 6 / Redundancy: 16.6 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 14.8 % / Rmerge(I) obs: 1.35 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ALK Resolution: 1.95→47.56 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.154 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.164 / 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: 30.146 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→47.56 Å
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Refine LS restraints |
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