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- PDB-6uww: Crystal structure of dihydrofolate reductase from Mycobacterium u... -

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Basic information

Entry
Database: PDB / ID: 6uww
TitleCrystal structure of dihydrofolate reductase from Mycobacterium ulcerans with P218 inhibitor
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / SSGCID / DHFR / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


dihydrofolate metabolic process / glycine biosynthetic 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 domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
Chem-MMV / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.92 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of dihydrofolate reductase from Mycobacterium ulcerans with SDDC-0001565 inhibitor
Authors: Mayclin, S.J. / Abendroth, J.A. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)20,3905
Polymers19,0941
Non-polymers1,2964
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.730, 66.200, 44.520
Angle α, β, γ (deg.)90.000, 91.614, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Dihydrofolate reductase


Mass: 19093.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium ulcerans (strain Agy99) (bacteria)
Strain: Agy99 / Gene: dfrA, MUL_2179 / Plasmid: MyulA.01062.a.B11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0PQG8, dihydrofolate reductase
#2: Chemical ChemComp-MMV / 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid


Mass: 360.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24N4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MORPHEUS E8 (305593e8): 12.5% (w/v) PEG1000, 12.t% (w/v) PEG3350, 12.5% (v/v) MPD, 30mM diethyleneglycol, 30mM triethyleneglycol, 30mM tetraethyleneglycol, 30mM pentaethyleneglycol, 100mM ...Details: MORPHEUS E8 (305593e8): 12.5% (w/v) PEG1000, 12.t% (w/v) PEG3350, 12.5% (v/v) MPD, 30mM diethyleneglycol, 30mM triethyleneglycol, 30mM tetraethyleneglycol, 30mM pentaethyleneglycol, 100mM MOPS/HEPES-Na pH7.5, 12.52mg/mL MyulA.01062.a.B11.PS38525, 4mM NADP, 4mM BSI4260, direct cryo, puck id:ogn0-3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.6888 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 0.92→50 Å / Num. obs: 112854 / % possible obs: 98.1 % / Redundancy: 3.451 % / Biso Wilson estimate: 11.486 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.043 / Χ2: 1.04 / Net I/σ(I): 14.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
0.92-0.942.9390.4912.0180420.7480.60594.7
0.94-0.973.4750.4082.7582090.8570.48599.2
0.97-13.5440.3073.7379960.9070.36399.3
1-1.033.5470.2334.8477540.9440.27699
1.03-1.063.5430.1666.6474800.9730.19698.9
1.06-1.13.5250.1298.4572330.9810.15398.7
1.1-1.143.5010.09810.8869520.9890.11698.1
1.14-1.193.4340.08212.8866620.9910.09798.1
1.19-1.243.1280.07313.4862950.9910.08896.3
1.24-1.33.5140.06616.1561700.9940.07899.1
1.3-1.373.6330.05818.2559460.9950.06999.7
1.37-1.453.6080.05220.5155820.9960.06199.7
1.45-1.563.5680.04523.5552450.9970.05399.5
1.56-1.683.540.03926.6449080.9970.04698.9
1.68-1.843.50.03529.3444220.9970.04197.9
1.84-2.063.360.03231.8539700.9970.03996.3
2.06-2.383.0420.0332.1633800.9970.03793.3
2.38-2.913.6780.02937.0330050.9980.03498
2.91-4.113.6270.02838.4323250.9980.03297.4
4.11-503.4850.02837.8912780.9980.03296.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX3423refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1df7

1df7


Resolution: 0.92→44.502 Å / SU ML: 0.0673 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.4304
RfactorNum. reflection% reflection
Rfree0.1454 2049 1.82 %
Rwork0.1315 --
obs0.1318 112838 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.08 Å2
Refinement stepCycle: LAST / Resolution: 0.92→44.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 0 36 255 1595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00951464
X-RAY DIFFRACTIONf_angle_d1.28892031
X-RAY DIFFRACTIONf_chiral_restr0.0863224
X-RAY DIFFRACTIONf_plane_restr0.0081256
X-RAY DIFFRACTIONf_dihedral_angle_d12.02971058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.92-0.940.22671440.21597028X-RAY DIFFRACTION94.01
0.94-0.960.2251430.18577436X-RAY DIFFRACTION99.1
0.96-0.990.17881410.15937512X-RAY DIFFRACTION99.33
0.99-1.020.14281310.1397422X-RAY DIFFRACTION99.08
1.02-1.050.14731210.12367436X-RAY DIFFRACTION98.9
1.05-1.090.1411370.11657411X-RAY DIFFRACTION98.83
1.09-1.130.11421550.10497345X-RAY DIFFRACTION98.23
1.13-1.190.10611200.10087396X-RAY DIFFRACTION98
1.19-1.250.11621230.10897295X-RAY DIFFRACTION96.41
1.25-1.330.14581140.11257488X-RAY DIFFRACTION99.63
1.33-1.430.12111370.11537510X-RAY DIFFRACTION99.69
1.43-1.570.12341650.11627456X-RAY DIFFRACTION99.48
1.57-1.80.14421600.137439X-RAY DIFFRACTION98.45
1.8-2.270.14751130.13847191X-RAY DIFFRACTION95.13
2.27-44.5020.15981450.1437424X-RAY DIFFRACTION97.2

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