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

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Basic information

Entry
Database: PDB / ID: 6dds
TitleMycobacterium tuberculosis Dihydrofolate Reductase complexed with beta-NADPH and 4-[3-[3-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]prop-2-ynyl]-5-methoxy-phenyl]benzoic 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
ACETATE ION / Chem-NDP / Chem-U75 / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsHajian, B. / Wright, D. / Scocchera, E.
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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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
C: Dihydrofolate reductase
D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,77819
Polymers70,6444
Non-polymers5,13415
Water10,323573
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8915
Polymers17,6611
Non-polymers1,2304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9014
Polymers17,6611
Non-polymers1,2403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9935
Polymers17,6611
Non-polymers1,3324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9935
Polymers17,6611
Non-polymers1,3324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.204, 60.804, 60.723
Angle α, β, γ (deg.)90.15, 89.94, 90.02
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 6 types, 588 molecules

#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-U75 / 4-[3-[3-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]prop-2-ynyl]-5-methoxy-phenyl]benzoic acid / 3'-(3-(2,4-diamino-6-ethylpyrimidin-5-yl)prop-2-yn-1-yl)-5'-methoxy-[1,1'-biphenyl]-4-carboxylic acid / UCP1175


Mass: 402.446 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H22N4O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / 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: 3.09 Å3/Da / Density % sol: 60.25 %
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: 1.72→27.004 Å / Num. obs: 70016 / % possible obs: 77.82 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.028 / Net I/σ(I): 23.3
Reflection shellResolution: 1.72→1.75 Å / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.128

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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: 1.72→27.004 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.04
RfactorNum. reflection% reflection
Rfree0.2056 2030 2.9 %
Rwork0.1817 --
obs0.1824 70016 77.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.72→27.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4976 0 347 573 5896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085484
X-RAY DIFFRACTIONf_angle_d1.2777490
X-RAY DIFFRACTIONf_dihedral_angle_d15.2371980
X-RAY DIFFRACTIONf_chiral_restr0.044774
X-RAY DIFFRACTIONf_plane_restr0.005947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7201-1.76310.30071670.22895224X-RAY DIFFRACTION83
1.7631-1.81070.27161330.20445295X-RAY DIFFRACTION85
1.8107-1.8640.23911450.19075319X-RAY DIFFRACTION85
1.864-1.92420.25481560.19484711X-RAY DIFFRACTION75
1.9242-1.99290.22441430.19325160X-RAY DIFFRACTION83
1.9929-2.07270.25861540.19035243X-RAY DIFFRACTION84
2.0727-2.1670.22591780.18345220X-RAY DIFFRACTION84
2.167-2.28120.19331040.18743373X-RAY DIFFRACTION54
2.2812-2.4240.19871290.19075195X-RAY DIFFRACTION82
2.424-2.6110.22211590.18935058X-RAY DIFFRACTION82
2.611-2.87350.19391600.20314998X-RAY DIFFRACTION81
2.8735-3.28870.22461400.18814989X-RAY DIFFRACTION80
3.2887-4.1410.18241290.16313974X-RAY DIFFRACTION64
4.141-27.00710.16771330.15614227X-RAY DIFFRACTION68

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