+Open data
-Basic information
Entry | Database: PDB / ID: 8jnw | ||||||
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Title | PfDXR - Mn2+ - NADPH - MAMK89 quaternary 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 / MOLECULAR REPLACEMENT / Resolution: 1.44 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 | 8jnw.cif.gz | 347 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jnw.ent.gz | 280.2 KB | Display | PDB format |
PDBx/mmJSON format | 8jnw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jnw_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8jnw_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8jnw_validation.xml.gz | 37.7 KB | Display | |
Data in CIF | 8jnw_validation.cif.gz | 56.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/8jnw ftp://data.pdbj.org/pub/pdb/validation_reports/jn/8jnw | HTTPS FTP |
-Related structure data
Related structure data | 8jnvC 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
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 634 molecules
#2: Chemical | #3: Chemical | #4: Chemical | Mass: 377.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24NO5P / Feature type: SUBJECT OF INVESTIGATION #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.39 Å3/Da / Density % sol: 48.49 % |
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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-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→63.93 Å / Num. obs: 153663 / % possible obs: 96.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 14.92 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.44→1.46 Å / Num. unique obs: 5311 / CC1/2: 0.805 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→63.93 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.017 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.063 / 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: 21.037 Å2
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Refinement step | Cycle: 1 / Resolution: 1.44→63.93 Å
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