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Yorodumi- PDB-6nnc: Structure of Dihydrofolate reductase from Mycobacterium tuberculo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nnc | ||||||
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Title | Structure of Dihydrofolate reductase from Mycobacterium tuberculosis in complex with NADPH and pemetrexed | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / antifolate | ||||||
Function / homology | Function and homology information dihydrofolate metabolic process / NADP+ binding / folic acid metabolic process / glycine biosynthetic 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Ribeiro, J.A. / Chavez-Pacheco, S.M. / Dias, M.V.B. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Crystal structures of the closed form of Mycobacterium tuberculosis dihydrofolate reductase in complex with dihydrofolate and antifolates. Authors: Ribeiro, J.A. / Chavez-Pacheco, S.M. / de Oliveira, G.S. / Silva, C.D.S. / Giudice, J.H.P. / Libreros-Zuniga, G.A. / 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 | 6nnc.cif.gz | 163 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nnc.ent.gz | 126.6 KB | Display | PDB format |
PDBx/mmJSON format | 6nnc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/6nnc ftp://data.pdbj.org/pub/pdb/validation_reports/nn/6nnc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17660.992 Da / Num. of mol.: 2 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 (E. coli) / References: UniProt: P9WNX1, dihydrofolate reductase |
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-Non-polymers , 5 types, 326 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #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: 2.22 Å3/Da / Density % sol: 44.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride |
-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: 1.4 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 25, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.4 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.8→46.75 Å / Num. obs: 29295 / % possible obs: 98.4 % / Redundancy: 12.6 % / Biso Wilson estimate: 18.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.019 / Rrim(I) all: 0.069 / Net I/σ(I): 29.7 / Num. measured all: 368144 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→32.159 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.36 / Stereochemistry target values: ML
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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: 100.89 Å2 / Biso mean: 26.1637 Å2 / Biso min: 10.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→32.159 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Origin x: 22.9291 Å / Origin y: 0.1282 Å / Origin z: 17.7536 Å
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Refinement TLS group |
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