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

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Basic information

Entry
Database: PDB / ID: 6ddp
TitleMycobacterium tuberculosis Dihydrofolate Reductase complexed with beta-NADPH and 3'-[(2R)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl]-5'-methoxy[1,1'-biphenyl]-4-carboxylic acid
ComponentsDihydrofolate reductase
Keywordsoxidoreductase/oxidoreductase inhibitor / DHFR / antifolate / oxidoreductase-oxidoreductase inhibitor complex
Function / homology
Function and homology information


NADP+ binding / dihydrofolate metabolic process / folic acid metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-G6Y / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsHajian, B. / 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
B: Dihydrofolate reductase
C: Dihydrofolate reductase
D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,29212
Polymers70,6444
Non-polymers4,6488
Water5,531307
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8233
Polymers17,6611
Non-polymers1,1622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8233
Polymers17,6611
Non-polymers1,1622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8233
Polymers17,6611
Non-polymers1,1622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8233
Polymers17,6611
Non-polymers1,1622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.770, 60.552, 60.637
Angle α, β, γ (deg.)90.04, 90.02, 90.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Dihydrofolate reductase


Mass: 17660.992 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-G6Y / 3'-[(2R)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl]-5'-methoxy[1,1'-biphenyl]-4-carboxylic acid


Mass: 416.472 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H24N4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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 Å3/Da / Density % sol: 59.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion
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: Jun 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.49→34.43 Å / Num. obs: 118402 / % possible obs: 83.15 % / Redundancy: 1.5 % / Rpim(I) all: 0.02 / Rsym value: 0.02 / Net I/σ(I): 19.6
Reflection shellResolution: 1.46→1.49 Å / Rpim(I) all: 0.239 / Rsym value: 0.239

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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: 1.49→34.424 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.61
RfactorNum. reflection% reflection
Rfree0.2253 2060 1.74 %
Rwork0.2029 --
obs0.2033 118402 83.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.49→34.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4976 0 316 307 5599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075499
X-RAY DIFFRACTIONf_angle_d1.2987529
X-RAY DIFFRACTIONf_dihedral_angle_d16.1121997
X-RAY DIFFRACTIONf_chiral_restr0.046784
X-RAY DIFFRACTIONf_plane_restr0.004956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4613-1.49530.30991700.27887957X-RAY DIFFRACTION85
1.4953-1.53270.30241360.24788083X-RAY DIFFRACTION87
1.5327-1.57410.18691360.23258123X-RAY DIFFRACTION86
1.5741-1.62050.25281100.22158058X-RAY DIFFRACTION87
1.6205-1.67280.24821520.21668107X-RAY DIFFRACTION86
1.6728-1.73260.17681350.21838010X-RAY DIFFRACTION86
1.7326-1.80190.2411600.21347866X-RAY DIFFRACTION85
1.8019-1.88390.27371460.21357965X-RAY DIFFRACTION85
1.8839-1.98320.22171350.2157882X-RAY DIFFRACTION85
1.9832-2.10750.25691540.20847804X-RAY DIFFRACTION84
2.1075-2.27020.20821280.20287775X-RAY DIFFRACTION83
2.2702-2.49860.22041070.21457665X-RAY DIFFRACTION82
2.4986-2.860.23171650.22097565X-RAY DIFFRACTION81
2.86-3.60260.21441070.19817352X-RAY DIFFRACTION79
3.6026-34.43390.20721190.16536130X-RAY DIFFRACTION66

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