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Yorodumi- PDB-8cq8: Mycobacterium tuberculosis dihydrofolate reductase in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cq8 | ||||||
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Title | Mycobacterium tuberculosis dihydrofolate reductase in complex with methyl 4-(2,6-diamino-5-(cyclopropylethynyl)pyrimidin-4-yl)benzoate | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Dihydrofolate reductase Mycobacterium tuberculosis | ||||||
Function / homology | Function and homology information dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kirkman, T.J. / Dias, M.V.B. / Coyne, A.G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Expansion of a series of pyrimidine derivatives utilising fragment-based merging leads to increased affinity to Mycobacterium tuberculosis dihydrofolate reductase (unpublished currently) Authors: Kirkman, T.J. / Dias, M.V.B. / Coyne, A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cq8.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cq8.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 8cq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cq8_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8cq8_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8cq8_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 8cq8_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/8cq8 ftp://data.pdbj.org/pub/pdb/validation_reports/cq/8cq8 | HTTPS FTP |
-Related structure data
Related structure data | 8cq9C 8cqaC 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: 17893.293 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: folA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E8UVJ4 |
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-Non-polymers , 6 types, 138 molecules
#2: Chemical | Mass: 308.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16N4O2 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / #7: 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: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6M ammonium sulphate, 100 mM MES, 10 mM CoCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→46.57 Å / Num. obs: 29939 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.024 / Rrim(I) all: 0.083 / Χ2: 1 / Net I/σ(I): 18.8 / Num. measured all: 370504 |
Reflection shell | Resolution: 1.8→1.84 Å / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 1.004 / Num. measured all: 21825 / Num. unique obs: 1737 / CC1/2: 0.843 / Rpim(I) all: 0.294 / Rrim(I) all: 1.047 / Χ2: 0.84 / Net I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.57 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.03 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→46.57 Å
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Refine LS restraints |
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LS refinement shell |
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