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

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Basic information

Entry
Database: PDB / ID: 6uwq
TitleCrystal structure of dihydrofolate reductase from Mycobacterium ulcerans with SDDC-0001565 inhibitor
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / SSGCID / DHFR / Structure-guided Drug Discovery Coalition / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


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 conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-QKJ / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle 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: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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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)20,2645
Polymers19,0361
Non-polymers1,2284
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.290, 70.750, 35.990
Angle α, β, γ (deg.)90.000, 110.991, 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: 19035.619 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.B13 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0PQG8, dihydrofolate reductase
#2: 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
#3: Chemical ChemComp-QKJ / 3-(3-{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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.83 Å3/Da / Density % sol: 32.75 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MyulA.01062.a.B13.PS38558 at 7.98mg/ml, incubated with 3 mM SDDC-0001565 and 3 mM NADP, mixed 1:1 with 100mM Bis-Tris:HCl pH6.5, 25% (w/v) PEG3350, 7.98mg/mL MyulA.01062.a.B13.PS38558. Tray: ...Details: MyulA.01062.a.B13.PS38558 at 7.98mg/ml, incubated with 3 mM SDDC-0001565 and 3 mM NADP, mixed 1:1 with 100mM Bis-Tris:HCl pH6.5, 25% (w/v) PEG3350, 7.98mg/mL MyulA.01062.a.B13.PS38558. Tray: 311137d2, puck: sxq1-11, cryoprotected with 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2018
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 21600 / % possible obs: 98.3 % / Redundancy: 3.701 % / Biso Wilson estimate: 21.78 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.042 / Χ2: 0.984 / Net I/σ(I): 21.55
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.543.6130.3283.7515580.9540.38696.3
1.54-1.583.5030.225.5714900.9630.2696
1.58-1.633.590.1647.2515060.9780.19295.7
1.63-1.683.7090.1259.4513970.9850.14696.1
1.68-1.733.7740.09811.7514040.990.11497.2
1.73-1.793.6640.07614.2613910.9930.08998.7
1.79-1.863.6030.06117.2113440.9960.07299.5
1.86-1.943.7280.05120.2712860.9970.05999.2
1.94-2.023.7730.04423.8912410.9970.05199.4
2.02-2.123.8320.04126.312000.9970.048100
2.12-2.243.7960.03628.8911280.9980.04299.5
2.24-2.373.6720.03430.2210550.9980.0499.8
2.37-2.543.7140.03332.3610090.9980.03999.6
2.54-2.743.8920.03133.639460.9980.03699.6
2.74-33.8520.02937.438660.9980.03399.3
3-3.353.6450.02739.867910.9990.03299.4
3.35-3.873.6740.02542.776780.9990.02999.4
3.87-4.743.9010.02545.795970.9990.02999.8
4.74-6.713.6040.02843.384550.9990.03398.7
6.71-503.5620.0344.332580.9980.03597.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX3602refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1df7

1df7


Resolution: 1.5→35.38 Å / SU ML: 0.2018 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.6561
RfactorNum. reflection% reflection
Rfree0.1788 1992 9.23 %
Rwork0.1314 --
obs0.1358 21592 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.47 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1252 0 82 203 1537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551419
X-RAY DIFFRACTIONf_angle_d0.91671952
X-RAY DIFFRACTIONf_chiral_restr0.0522212
X-RAY DIFFRACTIONf_plane_restr0.006269
X-RAY DIFFRACTIONf_dihedral_angle_d17.2802861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.40071460.40081350X-RAY DIFFRACTION95.96
1.54-1.580.32651370.25441339X-RAY DIFFRACTION96.22
1.58-1.630.23091390.15571382X-RAY DIFFRACTION95.9
1.63-1.680.18041320.12131341X-RAY DIFFRACTION96.34
1.68-1.740.1741230.12641425X-RAY DIFFRACTION97.42
1.74-1.810.20591450.1311409X-RAY DIFFRACTION98.92
1.81-1.890.17511340.12371403X-RAY DIFFRACTION99.42
1.89-1.990.17781430.1111410X-RAY DIFFRACTION99.68
1.99-2.110.17991610.11371412X-RAY DIFFRACTION99.87
2.11-2.280.18621420.11431415X-RAY DIFFRACTION99.68
2.28-2.510.18031410.1291419X-RAY DIFFRACTION99.94
2.51-2.870.17231480.13421437X-RAY DIFFRACTION99.87
2.87-3.610.1581620.12511417X-RAY DIFFRACTION99.75
3.61-35.380.14591390.12171441X-RAY DIFFRACTION99.43

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