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

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Basic information

Entry
Database: PDB / ID: 8coq
TitleMycobacterium tuberculosis dihydrofolate reductase in complex with 5-(cyclopropylethynyl)-6-(2-methoxyphenyl)pyrimidine-2,4-diamine
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 / : / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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Title: Currently unpublished
Authors: Kirkman, T.J. / Dias, M.V.B.
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,0529
Polymers35,7872
Non-polymers2,2657
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-44 kcal/mol
Surface area14740 Å2
Unit cell
Length a, b, c (Å)61.474, 72.810, 71.844
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, 159 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-VDT / 5-(2-cyclopropylethynyl)-6-(2-methoxyphenyl)pyrimidine-2,4-diamine


Mass: 280.324 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H16N4O / 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.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
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 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→51.14 Å / Num. obs: 47165 / % possible obs: 99.94 % / Redundancy: 13 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09159 / Rpim(I) all: 0.0268 / Net I/σ(I): 15.13
Reflection shellResolution: 1.7→1.761 Å / Rmerge(I) obs: 1.48 / Num. unique obs: 3538 / CC1/2: 0.818 / Rpim(I) all: 0.423

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.18.2_3874refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→51.14 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 1996 5.53 %
Rwork0.2103 --
obs0.2116 36110 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→51.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2626 0 7 152 2785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012705
X-RAY DIFFRACTIONf_angle_d1.5533704
X-RAY DIFFRACTIONf_dihedral_angle_d13.22390
X-RAY DIFFRACTIONf_chiral_restr0.071390
X-RAY DIFFRACTIONf_plane_restr0.011466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.32431420.31152358X-RAY DIFFRACTION100
1.74-1.790.24051450.27852396X-RAY DIFFRACTION100
1.79-1.840.28841350.26142416X-RAY DIFFRACTION100
1.84-1.90.271370.2382419X-RAY DIFFRACTION100
1.9-1.970.25021440.22622395X-RAY DIFFRACTION100
1.97-2.050.27331440.2272421X-RAY DIFFRACTION100
2.05-2.140.25151350.22122408X-RAY DIFFRACTION100
2.14-2.260.24841440.22252425X-RAY DIFFRACTION100
2.26-2.40.30871390.23152435X-RAY DIFFRACTION100
2.4-2.580.24591450.23362436X-RAY DIFFRACTION100
2.58-2.840.25911430.22362446X-RAY DIFFRACTION100
2.84-3.250.26571420.21272462X-RAY DIFFRACTION100
3.25-4.10.21151480.18892497X-RAY DIFFRACTION100
4.1-51.140.18521530.18392600X-RAY DIFFRACTION100

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