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

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Basic information

Entry
Database: PDB / ID: 8cox
TitleMycobacterium tuberculosis dihydrofolate reductase in complex with N-(2-(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: 2.1 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Title: Currently unpublished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)38,02410
Polymers35,7872
Non-polymers2,2378
Water79344
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-41 kcal/mol
Surface area15480 Å2
Unit cell
Length a, b, c (Å)61.481, 72.265, 72.843
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, 52 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
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#5: Chemical ChemComp-VBJ / ~{N}-[3-[2,6-bis(azanyl)-5-(2-cyclopropylethynyl)pyrimidin-4-yl]phenyl]methanesulfonamide


Mass: 343.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N5O2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 45.6 %
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: 2.1→46.98 Å / Num. obs: 19359 / % possible obs: 98.31 % / Redundancy: 11.6 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07102 / Rpim(I) all: 0.02241 / Rrim(I) all: 0.07463 / Net I/σ(I): 15.93
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 0.5218 / Num. unique obs: 1910 / CC1/2: 0.924 / CC star: 0.98 / Rpim(I) all: 0.1601 / Rrim(I) all: 0.5463

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.18.2_3874refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.98 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3006 1913 9.96 %
Rwork0.2378 --
obs0.2442 19211 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 137 44 2661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012689
X-RAY DIFFRACTIONf_angle_d1.2133684
X-RAY DIFFRACTIONf_dihedral_angle_d21.539388
X-RAY DIFFRACTIONf_chiral_restr0.064389
X-RAY DIFFRACTIONf_plane_restr0.008464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.4641340.42651207X-RAY DIFFRACTION98
2.15-2.210.43961370.38681241X-RAY DIFFRACTION100
2.21-2.270.52371080.4092976X-RAY DIFFRACTION78
2.28-2.350.41421370.31131216X-RAY DIFFRACTION99
2.35-2.430.32731360.27911245X-RAY DIFFRACTION100
2.43-2.530.3461370.25531216X-RAY DIFFRACTION100
2.53-2.640.36561380.27131261X-RAY DIFFRACTION100
2.65-2.780.35991370.27911259X-RAY DIFFRACTION100
2.78-2.960.38021400.27451234X-RAY DIFFRACTION100
2.96-3.190.35321390.25411260X-RAY DIFFRACTION100
3.19-3.510.29281370.23561262X-RAY DIFFRACTION100
3.51-4.010.27981400.21431261X-RAY DIFFRACTION100
4.02-5.060.22081420.1831295X-RAY DIFFRACTION100
5.06-46.980.26231510.21671365X-RAY DIFFRACTION100

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