[English] 日本語
Yorodumi- PDB-4alj: Crystal structure of S. aureus FabI in complex with NADP and 5-ch... -
+
Open data
-
Basic information
| Entry | Database: PDB / ID: 4alj | ||||||
|---|---|---|---|---|---|---|---|
| Title | Crystal structure of S. aureus FabI in complex with NADP and 5-chloro- 2-phenoxyphenol | ||||||
Components | ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH] | ||||||
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 | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Schiebel, J. / Chang, A. / Tonge, P.J. / Kisker, C. | ||||||
Citation | Journal: Structure / Year: 2012Title: Staphylococcus Aureus Fabi: Inhibition, Substrate Recognition and Potential Implications for in Vivo Essentiality Authors: Schiebel, J. / Chang, A. / Lu, H. / Baxter, M.V. / Tonge, P.J. / Kisker, C. | ||||||
| History |
|
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 4alj.cif.gz | 840 KB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb4alj.ent.gz | 703.7 KB | Display | PDB format |
| PDBx/mmJSON format | 4alj.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 4alj_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
|---|---|---|---|---|
| Full document | 4alj_full_validation.pdf.gz | 2.9 MB | Display | |
| Data in XML | 4alj_validation.xml.gz | 94.6 KB | Display | |
| Data in CIF | 4alj_validation.cif.gz | 126.7 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/4alj ftp://data.pdbj.org/pub/pdb/validation_reports/al/4alj | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 4aliC ![]() 4alkSC ![]() 4allC ![]() 4almC ![]() 4alnC C: citing same article ( S: Starting model for refinement |
|---|---|
| Similar structure data |
-
Links
-
Assembly
| Deposited unit | ![]()
| ||||||||
|---|---|---|---|---|---|---|---|---|---|
| 1 | ![]()
| ||||||||
| 2 | ![]()
| ||||||||
| Unit cell |
|
-
Components
| #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: A0A0H3JLH9*PLUS, EC: 1.3.1.10 #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-GLU / #4: Chemical | ChemComp-CH8 / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN B, LEU 2 TO VAL ENGINEERED ...ENGINEERED | |
|---|
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
|---|
-
Sample preparation
| Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.9 % / Description: NONE |
|---|---|
| Crystal grow | pH: 6.5 / Details: 0.1 M K/NA-PHOSPHATE PH 6.5, 35% MPD |
-Data collection
| Diffraction | Mean temperature: 100 K |
|---|---|
| Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 |
| Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 24, 2010 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
| Reflection | Resolution: 2.2→49.11 Å / Num. obs: 135192 / % possible obs: 94.4 % / Observed criterion σ(I): 6 / Redundancy: 1.85 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.91 |
| Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 1.85 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.95 / % possible all: 93.2 |
-
Processing
| Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 4ALK Resolution: 2.2→49.11 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.22 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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: 47.725 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 2.2→49.11 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refine LS restraints |
|
Movie
Controller
About Yorodumi




X-RAY DIFFRACTION
Citation














PDBj










