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- PDB-7k68: Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 7k68
TitleCrystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001565
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / SSGCID / SDDC / inhibitor / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-QKJ / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001565
Authors: Abendroth, J. / Dranow, D.M. / Santhakumar, V. / Walpole, C. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionSep 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1914
Polymers19,0521
Non-polymers1,1393
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.810, 66.480, 44.300
Angle α, β, γ (deg.)90.000, 92.014, 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: 19051.684 Da / Num. of mol.: 1 / Mutation: E96A
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.B12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0PQG8, dihydrofolate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus screen, condition D2: 10% w/v PEG 8000, 20% v/v ethylene glycol: 20mM of each 1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol: 100mM ...Details: Morpheus screen, condition D2: 10% w/v PEG 8000, 20% v/v ethylene glycol: 20mM of each 1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol: 100mM MES/imidazole pH 6.5: MyulA.01062.a.B12.PS38539 and 15.75mg/ml + 2.5mM NADP and 4mM SDDC compound SDDC-0001565: tray: 317892d2: cryo: direct: puck: xhf8-2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 29111 / % possible obs: 98.4 % / Redundancy: 5.017 % / Biso Wilson estimate: 18.119 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.026 / Rrim(I) all: 0.028 / Χ2: 0.969 / Net I/σ(I): 34.44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.45-1.492.5610.1825.2519870.9520.22291.6
1.49-1.533.6990.1627.720010.9750.18793.7
1.53-1.573.7880.1299.6320000.9820.14997.1
1.57-1.623.9660.11111.1819480.9880.12796.8
1.62-1.674.0580.10112.619260.990.11699.2
1.67-1.734.2510.08615.1118750.9930.09899.6
1.73-1.84.4020.07218.0418350.9950.082100
1.8-1.874.6990.05622.8917190.9970.06399.9
1.87-1.964.8520.04429.716920.9980.04999.9
1.96-2.055.0740.03934.8916080.9990.04399.9
2.05-2.165.2880.03341.2715250.9990.03799.9
2.16-2.295.340.0346.4114390.9990.03499.9
2.29-2.455.5330.02850.7213610.9990.03199.7
2.45-2.655.7220.02556.3912740.9990.027100
2.65-2.96.0260.02362.8117010.025100
2.9-3.246.5360.0274.73106110.02299.7
3.24-3.747.5630.01889.1592710.01999.9
3.74-4.599.9530.017112.478810.01899.9
4.59-6.4810.9860.018110.4962710.019100
6.48-5010.4830.019115.7134810.0299.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NAD and P218-bound structure, PDB entry 6uww

6uww


Resolution: 1.45→44.27 Å / SU ML: 0.1083 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.4394
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1585 1955 6.72 %0
Rwork0.1267 27152 --
obs0.1289 29107 98.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.47 Å2
Refinement stepCycle: LAST / Resolution: 1.45→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 75 230 1549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761443
X-RAY DIFFRACTIONf_angle_d1.0841990
X-RAY DIFFRACTIONf_chiral_restr0.0791215
X-RAY DIFFRACTIONf_plane_restr0.0129272
X-RAY DIFFRACTIONf_dihedral_angle_d14.7076557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.16541300.12661781X-RAY DIFFRACTION91.39
1.49-1.530.18191240.11781864X-RAY DIFFRACTION93.69
1.53-1.570.16651240.11391901X-RAY DIFFRACTION96.98
1.57-1.620.14851360.10561923X-RAY DIFFRACTION96.89
1.62-1.680.17151480.11381923X-RAY DIFFRACTION99.14
1.68-1.750.16531450.1121938X-RAY DIFFRACTION99.76
1.75-1.830.17471510.1211958X-RAY DIFFRACTION100
1.83-1.920.17421670.12821973X-RAY DIFFRACTION99.81
1.92-2.040.14831320.12361967X-RAY DIFFRACTION99.95
2.04-2.20.16911320.1221985X-RAY DIFFRACTION99.86
2.2-2.420.16391340.13151978X-RAY DIFFRACTION99.86
2.42-2.770.1831490.13951966X-RAY DIFFRACTION99.95
2.77-3.490.16471340.13991982X-RAY DIFFRACTION99.81
3.49-44.270.12391490.12562013X-RAY DIFFRACTION99.86

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