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

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Basic information

Entry
Database: PDB / ID: 6drs
TitleDihydrofolate Reductase (DHFR) of Aspergillus flavus in complex with a small molecule inhibitor
ComponentsDihydrofolate reductase, putative
KeywordsANTIFUNGAL PROTEIN/Inhibitor / Antifolate / DHFR / ANTIFUNGAL PROTEIN / ANTIFUNGAL PROTEIN-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
Chem-H8A / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.997 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 12, 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, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5518
Polymers27,9941
Non-polymers1,5577
Water2,882160
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)77.720, 77.720, 120.630
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, putative


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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-H8A / 3-{[(3R)-7,9-diamino-3-methyl-2,3-dihydrofuro[2,3-f]quinazolin-4-yl]oxy}benzonitrile


Mass: 333.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15N5O2
#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.: 160 / 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: 3.95 Å3/Da / Density % sol: 68.88 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.1 M MES monohydrate pH 6.0, 2.4 M 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 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.997→67.307 Å / Num. obs: 29252 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rpim(I) all: 0.047 / Rrim(I) all: 0.11 / Rsym value: 0.099 / Net I/av σ(I): 6.7 / Net I/σ(I): 11.4 / Num. measured all: 152553
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.997-2.115.10.3442.242010.1680.3840.344100
2.11-2.235.20.2762.839830.1330.3080.276100
2.23-2.395.20.2493.137480.1190.2770.249100
2.39-2.585.30.2093.735140.10.2330.209100
2.58-2.825.30.1634.832370.0780.1810.163100
2.82-3.165.30.1047.329290.0490.1160.104100
3.16-3.655.30.06111.626300.0290.0680.061100
3.65-4.475.30.0512.622320.0230.0550.05100
4.47-6.325.20.04313.117590.020.0480.043100
6.32-44.9194.70.0391110190.0210.0450.03998.1

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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: 1.997→44.96 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.895 / SU B: 4.713 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.145 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 1483 5.1 %RANDOM
Rwork0.219 ---
obs0.221 27733 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 120.55 Å2 / Biso mean: 26.04 Å2 / Biso min: 8.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.997→44.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 98 160 2115
Biso mean--37.25 29.83 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0151993
X-RAY DIFFRACTIONr_angle_refined_deg1.661.8362710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9745244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.98915.28353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2115278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7651516
X-RAY DIFFRACTIONr_chiral_restr0.1040.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211419
LS refinement shellResolution: 1.997→2.049 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 105 -
Rwork0.374 2030 -
all-2135 -
obs--99.86 %

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