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- PDB-6dtc: Dihydrofolate Reductase (DHFR) of Aspergillus flavus in complex w... -

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Basic information

Entry
Database: PDB / ID: 6dtc
TitleDihydrofolate Reductase (DHFR) of Aspergillus flavus in complex with a small molecule inhibitor
ComponentsDihydrofolate reductase
Keywordsantifungal protein/inhibitor / Antifolate / DHFR / antifungal protein / antifungal protein-inhibitor complex
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 / mitochondrion
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
Chem-H9G / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBensen, D.C. / Fortier, J.M. / Akers-Rodriguez, S. / Tari, L.W.
CitationJournal: To be published
Title: Prospecting for broad-spectrum inhibitors of fungal dihydrofolate reductase using a structure guided approach.
Authors: Bensen, D.C. / Fortier, J.M. / Akers-Rodriguez, S. / Tari, L.W.
History
DepositionJun 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: 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
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)29,4026
Polymers27,9941
Non-polymers1,4085
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-33 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.680, 77.680, 120.921
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Dihydrofolate reductase


Mass: 27994.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold)
Strain: ATCC 200026 / FGSC A1120 / NRRL 3357 / JCM 12722 / SRRC 167
Gene: AFLA_046100 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8NBN5
#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-H9G / (3R)-3-methyl-4-[3-(1H-tetrazol-5-yl)phenoxy]-2,3-dihydrofuro[2,3-f]quinazoline-7,9-diamine


Mass: 376.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16N8O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.96 Å3/Da / Density % sol: 68.93 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.1 M MES monohydrate pH 6.0, 2.4M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.997→67.273 Å / Num. all: 29063 / Num. obs: 29063 / % possible obs: 99.4 % / Redundancy: 2.8 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.084 / Rsym value: 0.068 / Net I/av σ(I): 7.1 / Net I/σ(I): 8 / Num. measured all: 80687
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2-2.112.70.2931.841250.2150.3660.29398.4
2.11-2.232.80.2083.739460.1470.2560.20899
2.23-2.392.80.1842.937170.1310.2270.18499.5
2.39-2.582.80.1395.534930.0970.1710.13999.7
2.58-2.822.80.1126.232420.0780.1380.11299.9
2.82-3.162.80.0671129200.0460.0820.067100
3.16-3.652.80.04414.526350.0310.0540.044100
3.65-4.472.80.0411322310.0290.0510.041100
4.47-6.322.80.03317.517590.0230.040.033100
6.32-44.9682.60.0418.19950.0320.0520.04196.6

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KYA

4kya


Resolution: 2→45.01 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.757 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.152 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 1473 5.1 %RANDOM
Rwork0.2135 ---
obs0.2162 27566 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.43 Å2 / Biso mean: 30.665 Å2 / Biso min: 11.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 2→45.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 91 197 2145
Biso mean--32.96 34.08 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121989
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.7252704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1765244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85621.23689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.31815341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2051516
X-RAY DIFFRACTIONr_chiral_restr0.1180.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021425
LS refinement shellResolution: 1.997→2.049 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 110 -
Rwork0.31 1976 -
all-2086 -
obs--97.39 %

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