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Yorodumi- PDB-3zhy: Structure of Mycobacterium tuberculosis DXR in complex with a di-... -
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-Basic information
Entry | Database: PDB / ID: 3zhy | |||||||||
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Title | Structure of Mycobacterium tuberculosis DXR in complex with a di- substituted fosmidomycin analogue | |||||||||
Components | 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE | |||||||||
Keywords | OXIDOREDUCTASE / RV2870C / DOXP/MEP PATHWAY / ISPC | |||||||||
Function / homology | Function and homology information terpenoid biosynthetic process, mevalonate-independent / 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 / cobalt ion binding / NADPH binding / manganese ion binding / magnesium ion binding Similarity search - Function | |||||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Bjorkelid, C. / Jansson, A.M. / Bergfors, T. / Unge, T. / Mowbray, S.L. / Jones, T.A. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Dxr Inhibition by Potent Mono- and Disubstituted Fosmidomycin Analogues. Authors: Jansson, A.M. / Wieckowska, A. / Bjorkelid, C. / Yahiaoui, S. / Sooriyaarachchi, S. / Lindh, M. / Bergfors, T. / Dharavath, S. / Desroses, M. / Suresh, S. / Andaloussi, M. / Nikhil, R. / ...Authors: Jansson, A.M. / Wieckowska, A. / Bjorkelid, C. / Yahiaoui, S. / Sooriyaarachchi, S. / Lindh, M. / Bergfors, T. / Dharavath, S. / Desroses, M. / Suresh, S. / Andaloussi, M. / Nikhil, R. / Sreevalli, S. / Srinivasa, B.R. / Larhed, M. / Jones, T.A. / Karlen, A. / Mowbray, S.L. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: The 1.9 A Resolution Structure of Mycobacterium Tuberculosis 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, a Potential Drug Target. Authors: Henriksson, L.M. / Bjorkelid, C. / Mowbray, S.L. / Unge, T. #2: Journal: J.Biol.Chem. / Year: 2007 Title: Structures of Mycobacterium Tuberculosis 1-Deoxy-D-Xylulose- 5-Phosphate Reductoisomerase Provide New Insights Into Catalysis. Authors: Henriksson, L.M. / Unge, T. / Carlsson, J. / Aqvist, J. / Mowbray, S.L. / Jones, T.A. #3: Journal: J.Med.Chem. / Year: 2011 Title: Design, Synthesis, and X-Ray Crystallographic Studies of Alpha-Aryl Substituted Fosmidomycin Analogues as Inhibitors of Mycobacterium Tuberculosis 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase. Authors: Andaloussi, M. / Henriksson, L.M. / Wieckowska, A. / Lindh, M. / Bjorkelid, C. / Larsson, A.M. / Suresh, S. / Iyer, H. / Srinivasa, B.R. / Bergfors, T. / Unge, T. / Mowbray, S.L. / Larhed, M. ...Authors: Andaloussi, M. / Henriksson, L.M. / Wieckowska, A. / Lindh, M. / Bjorkelid, C. / Larsson, A.M. / Suresh, S. / Iyer, H. / Srinivasa, B.R. / Bergfors, T. / Unge, T. / Mowbray, S.L. / Larhed, M. / Jones, T.A. / Karlen, A. #4: Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structural Studies on Mycobacterium Tuberculosis Dxr in Complex with the Antibiotic Fr-900098. Authors: Bjorkelid, C. / Bergfors, T. / Unge, T. / Mowbray, S.L. / Jones, T.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zhy.cif.gz | 154.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zhy.ent.gz | 121.5 KB | Display | PDB format |
PDBx/mmJSON format | 3zhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zhy_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 3zhy_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 3zhy_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 3zhy_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/3zhy ftp://data.pdbj.org/pub/pdb/validation_reports/zh/3zhy | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41599.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR References: UniProt: P64012, UniProt: P9WNS1*PLUS, 1-deoxy-D-xylulose-5-phosphate reductoisomerase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.56 Å3/Da / Density % sol: 51.95 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9552 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 3, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9552 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→58.23 Å / Num. obs: 39082 / % possible obs: 100 % / Observed criterion σ(I): 5 / Redundancy: 13.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→86.45 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.555 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES REFINED INDIVIDUALLY.
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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: 48.047 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→86.45 Å
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