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Yorodumi- PDB-6vvb: Mycobacterium tuberculosis dihydrofolate reductase in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vvb | ||||||
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Title | Mycobacterium tuberculosis dihydrofolate reductase in complex with 6-methyl-5-(4-phenylthiazol-2-yl)-2- (trifluoromethyl)nicotinic acid (fragment 10) | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / folate pathway | ||||||
Function / homology | Function and homology information NADP+ binding / 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: 1.45 Å | ||||||
Authors | Tyrakis, P. / 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 | 6vvb.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vvb.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 6vvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vvb_validation.pdf.gz | 433.1 KB | Display | wwPDB validaton report |
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Full document | 6vvb_full_validation.pdf.gz | 439.2 KB | Display | |
Data in XML | 6vvb_validation.xml.gz | 3 KB | Display | |
Data in CIF | 6vvb_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/6vvb ftp://data.pdbj.org/pub/pdb/validation_reports/vv/6vvb | HTTPS FTP |
-Related structure data
Related structure data | 6vs5C 6vs6C 6vs8C 6vs9C 6vsdC 6vseC 6vsfC 6vsgC 6vv6C 6vv7C 6vv8C 6vv9C 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17893.293 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: folA, dfrA, Rv2763c, MTV002.28c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WNX1, dihydrofolate reductase |
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#2: Chemical | ChemComp-RQ4 / |
#3: Chemical | ChemComp-P33 / |
#4: Chemical | ChemComp-NAP / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.44 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / Details: 8% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 20, 2011 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→31.2 Å / Num. obs: 27836 / % possible obs: 88.1 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Net I/σ(I): 15.3 / Num. measured all: 191518 / Scaling rejects: 23 | ||||||||||||||||||||||||||||||
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: 1.45→27.616 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2.13 / Phase error: 16.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.55 Å2 / Biso mean: 23.914 Å2 / Biso min: 8.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→27.616 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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