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Yorodumi- PDB-4d41: Crystal structure of S. aureus FabI in complex with NADP and 5-he... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 4d41 | ||||||
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| Title | Crystal structure of S. aureus FabI in complex with NADP and 5-hexyl- 2-(4-nitrophenoxy)phenol | ||||||
Components | ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH] | ||||||
Keywords | OXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE SUPERFAMILY / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / SAFABI / FABI | ||||||
| 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 | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Schiebel, J. / Chang, A. / Tonge, P.J. / Sotriffer, C.A. / Kisker, C. | ||||||
Citation | Journal: Biochemistry / Year: 2015Title: An Ordered Water Channel in Staphylococcus Aureus Fabi: Unraveling the Mechanism of Substrate Recognition and Reduction. Authors: Schiebel, J. / Chang, A. / Merget, B. / Bommineni, G.R. / Yu, W. / Spagnuolo, L.A. / Baxter, M.V. / Tareilus, M. / Tonge, P.J. / Kisker, C. / Sotriffer, C.A. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 4d41.cif.gz | 830.1 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb4d41.ent.gz | 696.2 KB | Display | PDB format |
| PDBx/mmJSON format | 4d41.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 4d41_validation.pdf.gz | 4.4 MB | Display | wwPDB validaton report |
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| Full document | 4d41_full_validation.pdf.gz | 4.4 MB | Display | |
| Data in XML | 4d41_validation.xml.gz | 89.6 KB | Display | |
| Data in CIF | 4d41_validation.cif.gz | 119.4 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/4d41 ftp://data.pdbj.org/pub/pdb/validation_reports/d4/4d41 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 4d42C ![]() 4d43C ![]() 4d44C ![]() 4d45C ![]() 4d46C ![]() 4alkS C: citing same article ( S: Starting model for refinement |
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| Similar structure data |
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Links
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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.) ![]() ![]() References: UniProt: Q7A6D8, UniProt: A0A0J9X1X7*PLUS, EC: 1.3.1.10 |
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-Non-polymers , 6 types, 958 molecules 










| #2: Chemical | ChemComp-MPD / ( #3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-JA1 / #5: Chemical | ChemComp-GLU / #6: Chemical | ChemComp-MRD / ( | #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: 2.92 Å3/Da / Density % sol: 57.89 % / Description: NONE |
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| Crystal grow | pH: 6.5 / Details: 0.1 M NA/K-PHOSPHATE PH 6.5, 47% 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 9, 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: 2.3→40.82 Å / Num. obs: 120978 / % possible obs: 96.8 % / Observed criterion σ(I): 6 / Redundancy: 2.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.1 |
| Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2 / % possible all: 96.1 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 4ALK Resolution: 2.3→40.82 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.829 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.198 / 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: 38.708 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.3→40.82 Å
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