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Yorodumi- PDB-6vv9: Mycobacterium tuberculosis dihydrofolate reductase in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vv9 | ||||||
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Title | Mycobacterium tuberculosis dihydrofolate reductase in complex with JEB300 | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / folate pathway | ||||||
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: 2.18 Å | ||||||
Authors | Ribeiro, J.A. / Chavez-Pacheco, S.M. / Dias, M.V.B. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2020 Title: Using a Fragment-Based Approach to Identify Alternative Chemical Scaffolds Targeting Dihydrofolate Reductase fromMycobacterium tuberculosis. Authors: Ribeiro, J.A. / Hammer, A. / Libreros-Zuniga, G.A. / Chavez-Pacheco, S.M. / Tyrakis, P. / de Oliveira, G.S. / Kirkman, T. / El Bakali, J. / Rocco, S.A. / Sforca, M.L. / Parise-Filho, R. / ...Authors: Ribeiro, J.A. / Hammer, A. / Libreros-Zuniga, G.A. / Chavez-Pacheco, S.M. / Tyrakis, P. / de Oliveira, G.S. / Kirkman, T. / El Bakali, J. / Rocco, S.A. / Sforca, M.L. / Parise-Filho, R. / Coyne, A.G. / Blundell, T.L. / Abell, C. / Dias, M.V.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vv9.cif.gz | 86.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vv9.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 6vv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vv9_validation.pdf.gz | 551.6 KB | Display | wwPDB validaton report |
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Full document | 6vv9_full_validation.pdf.gz | 558.9 KB | Display | |
Data in XML | 6vv9_validation.xml.gz | 3.4 KB | Display | |
Data in CIF | 6vv9_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/6vv9 ftp://data.pdbj.org/pub/pdb/validation_reports/vv/6vv9 | HTTPS FTP |
-Related structure data
Related structure data | 6vs5C 6vs6C 6vs8C 6vs9C 6vsdC 6vseC 6vsfC 6vsgC 6vv6C 6vv7C 6vv8C 6vvbC 1df7S 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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1 |
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2 |
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3 |
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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 (strain ATCC 25177 / H37Ra) (bacteria) Strain: ATCC 25177 / H37Ra / Gene: dfrA, MRA_2788 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A5U6B6, dihydrofolate reductase |
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-Non-polymers , 5 types, 98 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Chemical | #6: 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: 2.18 Å3/Da / Density % sol: 43.67 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: 1.6 M ammonium sulfate, 100 mM MES (2-(N-morpholino) ethanesulfonic acid), pH 6.5, 10 mM CoCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 27, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.45 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection twin | Operator: -h,l,k / Fraction: 0.22 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.18→46.64 Å / Num. obs: 16930 / % possible obs: 99.9 % / Redundancy: 9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.048 / Rrim(I) all: 0.148 / Net I/σ(I): 11 / Num. measured all: 152267 / Scaling rejects: 18 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1df7 Resolution: 2.18→38.963 Å / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.71 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.84 Å2 / Biso mean: 41.4927 Å2 / Biso min: 22.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.18→38.963 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 95 %
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