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- PDB-8cop: Mycobacterium tuberculosis dihydrofolate reductase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8cop
TitleMycobacterium tuberculosis dihydrofolate reductase in complex with N-(4-(2,6-diamino-5-(cyclopropylethynyl)pyrimidin-4-yl)phenyl)methanesulfonamide
ComponentsDihydrofolate reductase
KeywordsBIOSYNTHETIC PROTEIN / Mycobacterium tuberculosis Dihydrofolate reductase
Function / homology
Function and homology information


dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
: / Chem-NDP / PHOSPHATE ION / : / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKirkman, T.J. / Dias, M.V.B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI) United Kingdom
CitationJournal: To Be Published
Title: Expansion of a series of pyrimidine derivatives utilising fragment-based merging showcasing anleads to increased affinity with to Mycobacterium tuberculosis dihydrofolate reductase
Authors: Kirkmna, T.J. / Dias, M.V.B. / Coyne, A.
History
DepositionFeb 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,36711
Polymers35,7872
Non-polymers2,5809
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-34 kcal/mol
Surface area15180 Å2
Unit cell
Length a, b, c (Å)61.029, 71.927, 72.375
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dihydrofolate reductase


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 , 5 types, 65 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-VCI / ~{N}-[4-[2,6-bis(azanyl)-5-(2-cyclopropylethynyl)pyrimidin-4-yl]phenyl]methanesulfonamide


Mass: 343.403 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H17N5O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6M ammonium sulphate, 100 mM MES, 10 mM CoCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→46.66 Å / Num. obs: 30199 / % possible obs: 99.83 % / Redundancy: 12.5 % / CC1/2: 0.999 / Net I/σ(I): 10.82
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 2973 / CC1/2: 0.744

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.18.2_3874refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.66 Å / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 41.62 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2568 2010 6.66 %
Rwork0.1989 --
obs0.2133 30160 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 161 56 2705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012715
X-RAY DIFFRACTIONf_angle_d1.8843722
X-RAY DIFFRACTIONf_dihedral_angle_d25.167392
X-RAY DIFFRACTIONf_chiral_restr0.075390
X-RAY DIFFRACTIONf_plane_restr0.01466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.26521330.26341846X-RAY DIFFRACTION88
1.84-1.890.25171420.25322013X-RAY DIFFRACTION93
1.89-1.950.25411430.2561966X-RAY DIFFRACTION93
1.95-2.010.27981440.24512000X-RAY DIFFRACTION93
2.01-2.080.2721400.26431981X-RAY DIFFRACTION93
2.08-2.170.31911400.25211988X-RAY DIFFRACTION93
2.17-2.260.30161420.2512029X-RAY DIFFRACTION93
2.26-2.380.27471400.26131992X-RAY DIFFRACTION93
2.38-2.530.32641450.25822015X-RAY DIFFRACTION93
2.53-2.730.32781420.2512003X-RAY DIFFRACTION93
2.73-30.31771450.22252042X-RAY DIFFRACTION93
3-3.440.29661450.21022039X-RAY DIFFRACTION93
3.44-4.330.22481450.18212069X-RAY DIFFRACTION93
4.33-46.660.2311570.1682174X-RAY DIFFRACTION93

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