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Yorodumi- PDB-4y6p: Structure of Plasmodium falciparum DXR in complex with a beta-sub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y6p | ||||||
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Title | Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, RC177, and manganese | ||||||
Components | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplast | ||||||
Keywords | OXIDOREDUCTASE / enzyme-inhibitor complex / MEP pathway / isoprenoid biosynthesis | ||||||
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 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Sooriyaarachchi, S. / Bergfors, T. / Jones, T.A. / Mowbray, S.L. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: J.Med.Chem. / Year: 2015 Title: Synthesis and Bioactivity of beta-Substituted Fosmidomycin Analogues Targeting 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase. Authors: Chofor, R. / Sooriyaarachchi, S. / Risseeuw, M.D. / Bergfors, T. / Pouyez, J. / Johny, C. / Haymond, A. / Everaert, A. / Dowd, C.S. / Maes, L. / Coenye, T. / Alex, A. / Couch, R.D. / Jones, ...Authors: Chofor, R. / Sooriyaarachchi, S. / Risseeuw, M.D. / Bergfors, T. / Pouyez, J. / Johny, C. / Haymond, A. / Everaert, A. / Dowd, C.S. / Maes, L. / Coenye, T. / Alex, A. / Couch, R.D. / Jones, T.A. / Wouters, J. / Mowbray, S.L. / Van Calenbergh, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y6p.cif.gz | 192.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y6p.ent.gz | 149.6 KB | Display | PDB format |
PDBx/mmJSON format | 4y6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4y6p_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4y6p_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4y6p_validation.xml.gz | 37.4 KB | Display | |
Data in CIF | 4y6p_validation.cif.gz | 55.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/4y6p ftp://data.pdbj.org/pub/pdb/validation_reports/y6/4y6p | HTTPS FTP |
-Related structure data
Related structure data | 4y67SC 4y6rC 4y6sC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 1 / Auth seq-ID: 77 - 486 / Label seq-ID: 11 - 420
NCS oper:
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48164.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: mature protein lacks signal and apicoplast-targeting sequences Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: DXR, PF14_0641 / Plasmid: pEXP-5-CT/TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 References: UniProt: Q8IKG4, 1-deoxy-D-xylulose-5-phosphate reductoisomerase |
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-Non-polymers , 5 types, 579 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.03M MgCl2, 0.03M CaCl2, 0.1M MOPS/Hepes-Na pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97856 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 27, 2014 / Details: mirrors |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.47 Å / Num. obs: 65358 / % possible obs: 95.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 3 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Y67 Resolution: 1.9→48.47 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.174 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.131 / 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: 21.648 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→48.47 Å
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Refine LS restraints |
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