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- PDB-4igf: Crystal structure of Plasmodium falciparum FabI complexed with NA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4igf | ||||||
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Title | Crystal structure of Plasmodium falciparum FabI complexed with NAD and inhibitor 3-(4-Chloro-2-hydroxyphenoxy)-7-hydroxy-2H-chromen-2-one | ||||||
![]() | Enoyl-acyl carrier reductase | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Reductase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | ![]() apicoplast / enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kostrewa, D. / Perozzo, R. | ||||||
![]() | ![]() Title: Design, Synthesis, and Biological and Crystallographic Evaluation of Novel Inhibitors of Plasmodium falciparum Enoyl-ACP-reductase (PfFabI) Authors: Belluti, F. / Perozzo, R. / Lauciello, L. / Colizzi, F. / Kostrewa, D. / Bisi, A. / Gobbi, S. / Rampa, A. / Bolognesi, M.L. / Recanatini, M. / Brun, R. / Scapozza, L. / Cavalli, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 245.2 KB | Display | ![]() |
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PDB format | ![]() | 197 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 25.3 KB | Display | |
Data in CIF | ![]() | 35.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4igeC ![]() 1nhgS 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39269.262 Da / Num. of mol.: 2 / Fragment: C-terminal fragment, UNP residues 96-432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 3D7 / Gene: PfENR, PFF0730c / Plasmid: pET28a / Production host: ![]() ![]() References: UniProt: C6KSZ2, enoyl-[acyl-carrier-protein] reductase (NADH) |
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-Non-polymers , 5 types, 252 molecules ![](data/chem/img/CHV.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 5.6 Details: 0.1M MES, 2.35M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Details: mirrors |
Radiation | Monochromator: Bartels monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→70 Å / Num. all: 32749 / Num. obs: 32749 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.73 % / Biso Wilson estimate: 41 Å2 / Rsym value: 0.135 / Net I/σ(I): 22.48 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 14.91 % / Mean I/σ(I) obs: 3.27 / Num. unique all: 2389 / Rsym value: 1.09 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1NHG Resolution: 2.3→69.976 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.25 Isotropic thermal model: TLS groups for protein chains A and B, individual isotropic temperature factors Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.06 / Stereochemistry target values: Engh & Huber Details: Mask bulk solvent model. Maximum-likelhood based coordinate error 0.25 A.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 152.99 Å2 / Biso mean: 30.9842 Å2 / Biso min: 2.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→69.976 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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