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- PDB-5ja3: Mycobacterium tuberculosis Dihydrofolate Reductase complexed with... -

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Basic information

Entry
Database: PDB / ID: 5ja3
TitleMycobacterium tuberculosis Dihydrofolate Reductase complexed with beta- NADPH and 3'-(3-(2,4-diamino-6-ethylpyrimidin-5-yl)prop-2-yn-1-yl)-4'-methoxy-[1,1'-b iphenyl]-4-carboxylic acid (UCP1106)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / dhfr / antifolate / folate pathway
Function / homology
Function and homology information


NADP+ binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / folic acid metabolic process / 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-NDP / Chem-U06 / Dihydrofolate reductase / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.814 Å
AuthorsHajian, B. / Anderson, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI111957 United States
CitationJournal: Plos One / Year: 2016
Title: Propargyl-Linked Antifolates Are Potent Inhibitors of Drug-Sensitive and Drug-Resistant Mycobacterium tuberculosis.
Authors: Hajian, B. / Scocchera, E. / Keshipeddy, S. / G-Dayanandan, N. / Shoen, C. / Krucinska, J. / Reeve, S. / Cynamon, M. / Anderson, A.C. / Wright, D.L.
History
DepositionApr 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)75,23512
Polymers70,6444
Non-polymers4,5918
Water70339
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.612, 60.444, 60.472
Angle α, β, γ (deg.)90.07, 90.06, 89.93
Int Tables number1
Space group name H-MP1
Detailstetramer according to gel filtration

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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 (bacteria) / Strain: CDC 1551 / Oshkosh / Gene: folA, dfrA, MT2833 / Plasmid: pET41-a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P9WNX0, UniProt: P9WNX1*PLUS, dihydrofolate reductase
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-U06 / 4-[3-[3-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]prop-2-ynyl]-4-methoxy-phenyl]benzoic acid / 3'-(3-(2,4-diamino-6-ethylpyrimidin-5-yl)prop-2-yn-1-yl)-4'-methoxy-[1,1'-biphenyl]-4-carboxylic acid / UCP1106


Mass: 402.446 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H22N4O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / 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 / Ambient temp details: liquid nitrogen cryo
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 10, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.814→34.725 Å / Num. obs: 55796 / % possible obs: 72.89 % / Redundancy: 1.5 % / Rsym value: 0.034 / Net I/σ(I): 28.82

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.814→34.725 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.54
RfactorNum. reflection% reflection
Rfree0.2671 1962 3.52 %
Rwork0.2251 --
obs0.2266 55796 72.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.814→34.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4976 0 312 39 5327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095441
X-RAY DIFFRACTIONf_angle_d1.3667441
X-RAY DIFFRACTIONf_dihedral_angle_d15.4471963
X-RAY DIFFRACTIONf_chiral_restr0.046774
X-RAY DIFFRACTIONf_plane_restr0.005941
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8136-1.8590.29451440.23634027X-RAY DIFFRACTION75
1.859-1.90930.25461360.24414033X-RAY DIFFRACTION77
1.9093-1.96540.28511570.24064086X-RAY DIFFRACTION77
1.9654-2.02890.36021440.2534034X-RAY DIFFRACTION77
2.0289-2.10140.31541160.25514005X-RAY DIFFRACTION76
2.1014-2.18550.26861460.24964010X-RAY DIFFRACTION76
2.1855-2.28490.28941580.24333959X-RAY DIFFRACTION75
2.2849-2.40540.29461600.24583914X-RAY DIFFRACTION75
2.4054-2.5560.33071280.23463854X-RAY DIFFRACTION74
2.556-2.75330.24051560.24273885X-RAY DIFFRACTION73
2.7533-3.03020.27681550.25573742X-RAY DIFFRACTION72
3.0302-3.46840.25791160.23953664X-RAY DIFFRACTION69
3.4684-4.36840.26341040.20033433X-RAY DIFFRACTION65
4.3684-34.7310.22651420.17653188X-RAY DIFFRACTION61

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