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Yorodumi- PDB-2cig: Dihydrofolate reductase from Mycobacterium tuberculosis inhibited... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cig | ||||||
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Title | Dihydrofolate reductase from Mycobacterium tuberculosis inhibited by the acyclic 4R isomer of INH-NADP a derivative of the prodrug isoniazid. | ||||||
Components | DIHYDROFOLATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / NADP / ISONIAZID / REDUCTASE / INHIBITOR / BISUBSTRATE / TUBERCULOSIS / ONE-CARBON METABOLISM | ||||||
Function / homology | Function and homology information glycine biosynthetic process / NADP+ binding / dihydrofolate metabolic process / folic acid metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Argyrou, A. / Vetting, M.W. / Aladegbami, B. / Blanchard, J.S. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2006 Title: Mycobacterium Tuberculosis Dihydrofolate Reductase is a Target for Isoniazid Authors: Argyrou, A. / Vetting, M.W. / Aladegbami, B. / Blanchard, J.S. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cig.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cig.ent.gz | 35.8 KB | Display | PDB format |
PDBx/mmJSON format | 2cig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cig_validation.pdf.gz | 765.3 KB | Display | wwPDB validaton report |
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Full document | 2cig_full_validation.pdf.gz | 768.7 KB | Display | |
Data in XML | 2cig_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 2cig_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/2cig ftp://data.pdbj.org/pub/pdb/validation_reports/ci/2cig | HTTPS FTP |
-Related structure data
Related structure data | 1df7S 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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-Components
#1: Protein | Mass: 17659.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0A546, UniProt: P9WNX1*PLUS, dihydrofolate reductase | ||||
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#2: Chemical | ChemComp-1DG / ( | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.1 % |
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Crystal grow | pH: 4.5 Details: 1.6 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE, PH 4.6, 10 % GLYCEROL |
-Data collection
Diffraction | Mean temperature: 194 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200B / Wavelength: 1.5418 |
Detector | Type: MSC R-AXIS IV / Detector: IMAGE PLATE / Date: Jul 7, 2005 / Details: OSMIC CONFOCAL MAXFLUX OPTICS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 84102 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.26 / 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 1DF7 Resolution: 1.9→60.63 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.772 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.124 / 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: 24.04 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→60.63 Å
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Refine LS restraints |
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