+Open data
-Basic information
Entry | Database: PDB / ID: 8jnv | ||||||
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Title | PfDXR - Mn2+ - MAMK89 ternary complex | ||||||
Components | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | ||||||
Keywords | ISOMERASE / Inhibitor / Complex | ||||||
Function / homology | Function and homology information apicoplast / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process / 1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / NADPH binding / manganese ion binding Similarity search - Function | ||||||
Biological species | Plasmodium falciparum HB3 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Takada, S. / Sakamoto, Y. / Tanaka, N. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2024 Title: Reverse N -Substituted Hydroxamic Acid Derivatives of Fosmidomycin Target a Previously Unknown Subpocket of 1-Deoxy-d-xylulose 5-Phosphate Reductoisomerase (DXR). Authors: Abdullaziz, M.A. / Takada, S. / Illarionov, B. / Pessanha de Carvalho, L. / Sakamoto, Y. / Hofmann, S. / Knak, T. / Kiffe-Delf, A.L. / Mazzone, F. / Pfeffer, K. / Kalscheuer, R. / Bacher, A. ...Authors: Abdullaziz, M.A. / Takada, S. / Illarionov, B. / Pessanha de Carvalho, L. / Sakamoto, Y. / Hofmann, S. / Knak, T. / Kiffe-Delf, A.L. / Mazzone, F. / Pfeffer, K. / Kalscheuer, R. / Bacher, A. / Held, J. / Fischer, M. / Tanaka, N. / Kurz, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jnv.cif.gz | 337.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jnv.ent.gz | 272.9 KB | Display | PDB format |
PDBx/mmJSON format | 8jnv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jnv_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 8jnv_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 8jnv_validation.xml.gz | 36 KB | Display | |
Data in CIF | 8jnv_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/8jnv ftp://data.pdbj.org/pub/pdb/validation_reports/jn/8jnv | HTTPS FTP |
-Related structure data
Related structure data | 8jnwC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46830.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum HB3 (eukaryote) / Gene: DXR / Production host: Escherichia coli (E. coli) References: UniProt: O96693, 1-deoxy-D-xylulose-5-phosphate reductoisomerase #2: Chemical | #3: Chemical | Mass: 377.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24NO5P / Feature type: SUBJECT OF INVESTIGATION #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.36 Å3/Da / Density % sol: 47.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl pH 8.0, 20%(w/v) PEG6000, and 0.2 M CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 9, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→63.39 Å / Num. obs: 111671 / % possible obs: 97.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 15.15 Å2 / CC1/2: 0.974 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5457 / CC1/2: 0.771 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→63.31 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.481 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.083 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.958 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→63.31 Å
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