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

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Basic information

Entry
Database: PDB / ID: 8cow
TitleMycobacterium tuberculosis dihydrofolate reductase in complex with 5-(cyclopropylethynyl)-6-(2-fluorophenyl)pyrimidine-2,4-diamine
ComponentsDihydrofolate reductase
KeywordsBIOSYNTHETIC PROTEIN / Mycobacterium tuberculosis Dihydrofolate reductase
Function / homology
Function and homology information


NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / 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 / : / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKirkman, T.J. / Dias, M.V.B. / Coyne, A.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI) United Kingdom
CitationJournal: To Be Published
Title: Currently unpublished
Authors: Kirkman, T.J. / Dias, M.V.B.
History
DepositionMar 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 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)38,12410
Polymers35,7872
Non-polymers2,3378
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-62 kcal/mol
Surface area14740 Å2
Unit cell
Length a, b, c (Å)61.104, 72.507, 71.794
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, 237 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-VB0 / 5-(2-cyclopropylethynyl)-6-(2-fluorophenyl)pyrimidine-2,4-diamine


Mass: 268.289 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13FN4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 44.65 %
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: Mar 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→51.02 Å / Num. obs: 42774 / % possible obs: 98.28 % / Redundancy: 12.6 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1101 / Rpim(I) all: 0.03266 / Rrim(I) all: 0.1149 / Net I/σ(I): 8.57
Reflection shellResolution: 1.6→1.657 Å / Rmerge(I) obs: 1.228 / Mean I/σ(I) obs: 8.57 / Num. unique obs: 4206 / CC1/2: 0.79 / CC star: 0.94 / Rpim(I) all: 0.3513

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.18.2_3874refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→51.02 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2555 1976 4.7 %
Rwork0.2161 --
obs0.218 42039 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→51.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 148 229 2860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092703
X-RAY DIFFRACTIONf_angle_d1.4863701
X-RAY DIFFRACTIONf_dihedral_angle_d16.883392
X-RAY DIFFRACTIONf_chiral_restr0.065391
X-RAY DIFFRACTIONf_plane_restr0.009468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.42881190.42142255X-RAY DIFFRACTION79
1.64-1.680.4231300.40182787X-RAY DIFFRACTION97
1.68-1.730.35761470.36842868X-RAY DIFFRACTION100
1.73-1.790.35621400.34832886X-RAY DIFFRACTION100
1.79-1.850.35371380.29762883X-RAY DIFFRACTION100
1.85-1.930.30431430.24392862X-RAY DIFFRACTION100
1.93-2.020.27651410.21362891X-RAY DIFFRACTION100
2.02-2.120.25741400.21842893X-RAY DIFFRACTION100
2.12-2.260.29551410.20792908X-RAY DIFFRACTION100
2.26-2.430.27591440.2112908X-RAY DIFFRACTION100
2.43-2.670.23731430.21052904X-RAY DIFFRACTION100
2.67-3.060.27261490.21012947X-RAY DIFFRACTION100
3.06-3.860.22841440.18542966X-RAY DIFFRACTION100
3.86-51.020.20751570.19463105X-RAY DIFFRACTION100

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