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- PDB-6ddw: Mycobacterium tuberculosis Dihydrofolate Reductase complexed with... -

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Basic information

Entry
Database: PDB / ID: 6ddw
TitleMycobacterium tuberculosis Dihydrofolate Reductase complexed with beta-NADPH and N-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}-2-hydroxybenzene-1-carbonyl)-L-glutamic acid
ComponentsDihydrofolate reductase
Keywordsoxidoreductase/oxidoreductase inhibitor / DHFR / Antifolate / oxidoreductase-oxidoreductase inhibitor complex
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 / NADP binding / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-G7D / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHajian, B. / Scocchera, E. / Wright, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI104841 United States
CitationJournal: Cell Chem Biol / Year: 2019
Title: Drugging the Folate Pathway in Mycobacterium tuberculosis: The Role of Multi-targeting Agents.
Authors: Hajian, B. / Scocchera, E. / Shoen, C. / Krucinska, J. / Viswanathan, K. / G-Dayanandan, N. / Erlandsen, H. / Estrada, A. / Mikusova, K. / Kordulakova, J. / Cynamon, M. / Wright, D.
History
DepositionMay 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5618
Polymers17,8931
Non-polymers1,6677
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.439, 60.439, 58.959
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dihydrofolate reductase


Mass: 17893.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: folA, dfrA, Rv2763c, MTV002.28c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WNX1, dihydrofolate reductase

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Non-polymers , 5 types, 144 molecules

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


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-G7D / N-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}-2-hydroxybenzene-1-carbonyl)-L-glutamic acid


Mass: 457.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N7O7
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 137 / Source method: isolated from a natural source / Formula: H2O

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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: 3.01 Å3/Da / Density % sol: 59.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.5
Details: 2.1-2.3 M ammonium sulfate, 0.1 M sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→42.204 Å / Num. obs: 36214 / % possible obs: 86.62 % / Redundancy: 2 % / Rmerge(I) obs: 0.013 / Rpim(I) all: 0.013 / Net I/σ(I): 24
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.151

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JA3

5ja3


Resolution: 1.4→42.204 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 28.96
RfactorNum. reflection% reflection
Rfree0.2116 1566 4.32 %
Rwork0.1845 --
obs0.1857 36214 86.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→42.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 110 137 1491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071386
X-RAY DIFFRACTIONf_angle_d1.3691889
X-RAY DIFFRACTIONf_dihedral_angle_d14.346506
X-RAY DIFFRACTIONf_chiral_restr0.075194
X-RAY DIFFRACTIONf_plane_restr0.006236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4001-1.44530.3204430.24851596X-RAY DIFFRACTION43
1.4453-1.4970.21811010.21172039X-RAY DIFFRACTION57
1.497-1.55690.21861660.19722929X-RAY DIFFRACTION81
1.5569-1.62780.2151030.19053492X-RAY DIFFRACTION95
1.6278-1.71360.20631740.18813467X-RAY DIFFRACTION96
1.7136-1.8210.19951360.19083545X-RAY DIFFRACTION97
1.821-1.96160.22051850.18973388X-RAY DIFFRACTION94
1.9616-2.1590.23071540.19733562X-RAY DIFFRACTION98
2.159-2.47130.21991610.20373570X-RAY DIFFRACTION98
2.4713-3.11350.21011900.20073447X-RAY DIFFRACTION95
3.1135-42.22310.2021530.16183613X-RAY DIFFRACTION97

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