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Yorodumi- PDB-4a03: Crystal Structure of Mycobacterium tuberculosis DXR in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a03 | ||||||
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Title | Crystal Structure of Mycobacterium tuberculosis DXR in complex with the antibiotic FR900098 and cofactor NADPH | ||||||
Components | 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE | ||||||
Keywords | OXIDOREDUCTASE / FR900098 / MEP PATHWAY | ||||||
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: 1.65 Å | ||||||
Authors | Bjorkelid, C. / Bergfors, T. / Jones, T.A. | ||||||
Citation | 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 | 4a03.cif.gz | 167.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a03.ent.gz | 130.9 KB | Display | PDB format |
PDBx/mmJSON format | 4a03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a03_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4a03_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4a03_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 4a03_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/4a03 ftp://data.pdbj.org/pub/pdb/validation_reports/a0/4a03 | HTTPS FTP |
-Related structure data
Related structure data | 2jcz S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.15, -0.0909, -0.9845), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41700.973 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-389 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PEXP5CT/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI References: UniProt: P64012, UniProt: P9WNS1*PLUS, 1-deoxy-D-xylulose-5-phosphate reductoisomerase |
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-Non-polymers , 5 types, 536 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: 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: 2.44 Å3/Da / Density % sol: 49.66 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: SITTING-DROP VAPOR-DIFFUSION METHOD AT 293 K. 10% (W/V) PEG 20000, 20% (V/V) MONOMETHYL ETHER PEG 550, 0.1 M MES/IMIDAZOLE, PH 6.5, AND 0.03 M EACH OF DIETHYLENEGLYCOL, TRIETHYLENEGLYCOL, ...Details: SITTING-DROP VAPOR-DIFFUSION METHOD AT 293 K. 10% (W/V) PEG 20000, 20% (V/V) MONOMETHYL ETHER PEG 550, 0.1 M MES/IMIDAZOLE, PH 6.5, AND 0.03 M EACH OF DIETHYLENEGLYCOL, TRIETHYLENEGLYCOL, TETRAETHYLENEGLYCOL AND PENTAETHYLENEGLYCOL. |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9768 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9768 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→42.21 Å / Num. obs: 101922 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JCZ 2jcz Resolution: 1.65→42.21 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.659 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.092 / 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: 22.132 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→42.21 Å
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Refine LS restraints |
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