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

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Basic information

Entry
Database: PDB / ID: 8cqa
TitleMycobacterium tuberculosis dihydrofolate reductase in complex with N-(4-(2,6-diamino-5-(cyclopropylethynyl)pyrimidin-4-yl)phenyl)acetamide
ComponentsDihydrofolate reductase
KeywordsBIOSYNTHETIC PROTEIN / Dihydrofolate reductase Mycobacterium tuberculosis
Function / homology: / Chem-NDP / : / :
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: Expansion of a series of pyrimidine derivatives utilising fragment-based merging leads to increased affinity to Mycobacterium tuberculosis dihydrofolate reductase (unpublished currently)
Authors: Kirkman, T.J. / Dias, M.V.B. / Coyne, A.G.
History
DepositionMar 4, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,13313
Polymers35,3222
Non-polymers2,81111
Water95553
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-59 kcal/mol
Surface area15310 Å2
Unit cell
Length a, b, c (Å)61.349, 72.058, 72.248
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: 17660.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: E5M05_04710 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3E0UVM8

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Non-polymers , 6 types, 64 molecules

#2: Chemical ChemComp-VF6 / ~{N}-[4-[2,6-bis(azanyl)-5-(2-cyclopropylethyl)pyrimidin-4-yl]phenyl]ethanamide


Mass: 311.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N5O / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#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.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.26 Å3/Da / Density % sol: 45.59 %
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 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→46.76 Å / Num. obs: 22315 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rpim(I) all: 0.025 / Rrim(I) all: 0.091 / Net I/σ(I): 14.9 / Num. measured all: 283162
Reflection shellResolution: 2→2.11 Å / % possible obs: 100 % / Redundancy: 12.7 % / Num. measured all: 40858 / Num. unique obs: 3215 / CC1/2: 0.834 / Rpim(I) all: 0.342 / Rrim(I) all: 1.234 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.18.2_3874refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.76 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.06 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2756 1075 4.83 %
Rwork0.2067 --
obs0.2324 22260 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→46.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 176 53 2717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142732
X-RAY DIFFRACTIONf_angle_d1.4783738
X-RAY DIFFRACTIONf_dihedral_angle_d24.193397
X-RAY DIFFRACTIONf_chiral_restr0.073386
X-RAY DIFFRACTIONf_plane_restr0.01472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.40791260.37112605X-RAY DIFFRACTION95
2.09-2.20.3931030.36022648X-RAY DIFFRACTION96
2.2-2.340.38211260.36772610X-RAY DIFFRACTION95
2.34-2.520.37781310.32962602X-RAY DIFFRACTION95
2.52-2.770.38521410.30282650X-RAY DIFFRACTION95
2.77-3.170.33641370.25062619X-RAY DIFFRACTION95
3.17-40.30161540.20782662X-RAY DIFFRACTION94
4-46.760.26011540.15282792X-RAY DIFFRACTION95

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