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- PDB-1aoe: CANDIDA ALBICANS DIHYDROFOLATE REDUCTASE COMPLEXED WITH DIHYDRO-N... -

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Basic information

Entry
Database: PDB / ID: 1aoe
TitleCANDIDA ALBICANS DIHYDROFOLATE REDUCTASE COMPLEXED WITH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NADPH) AND 1,3-DIAMINO-7-(1-ETHYEPROPYE)-7H-PYRRALO-[3,2-F]QUINAZOLINE (GW345)
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / ANTIFUNGAL TARGET / REDUCTASE
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, subunit A / Dihydrofolate Reductase, subunit A / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-GW3 / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / DIRECT REPLACEMENT / Resolution: 1.6 Å
AuthorsWhitlow, M. / Howard, A.J. / Stewart, D.
Citation
Journal: J.Biol.Chem. / Year: 1997
Title: X-ray crystallographic studies of Candida albicans dihydrofolate reductase. High resolution structures of the holoenzyme and an inhibited ternary complex.
Authors: Whitlow, M. / Howard, A.J. / Stewart, D. / Hardman, K.D. / Kuyper, L.F. / Baccanari, D.P. / Fling, M.E. / Tansik, R.L.
#1: Journal: J.Med.Chem. / Year: 1996
Title: High-Affinity Inhibitors of Dihydrofolate Reductase: Antimicrobial and Anticancer Activities of 7,8-Dialkyl-1,3-Diaminopyrrolo[3,2-F]Quinazolines with Small Molecular Size
Authors: Kuyper, L.F. / Baccanari, D.P. / Jones, M.L. / Hunter, R.N. / Tansik, R.L. / Joyner, S.S. / Boytos, C.M. / Rudolph, S.K. / Knick, V. / Wilson, H.R. / Caddell, J.M. / Friedman, H.S. / Comley, J.C. / Stables, J.N.
#2: Journal: J.Biol.Chem. / Year: 1989
Title: Characterization of Candida Albicans Dihydrofolate Reductase
Authors: Baccanari, D.P. / Tansik, R.L. / Joyner, S.S. / Fling, M.E. / Smith, P.L. / Freisheim, J.H.
History
DepositionJul 2, 1997Processing site: BNL
Revision 1.0Jan 7, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROFOLATE REDUCTASE
B: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4196
Polymers44,3892
Non-polymers2,0304
Water5,999333
1
A: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2093
Polymers22,1951
Non-polymers1,0152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2093
Polymers22,1951
Non-polymers1,0152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.910, 67.280, 38.490
Angle α, β, γ (deg.)90.00, 93.07, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.712, 0.249, 0.656), (-0.236, -0.796, 0.558), (0.661, -0.552, -0.508)
Vector: 2.407, 17.907, 25.074)

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Components

#1: Protein DIHYDROFOLATE REDUCTASE / / DHFR


Mass: 22194.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Cell line: BL21 / Plasmid: BL21 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P22906, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-GW3 / 7-(1-ETHYL-PROPYL)-7H-PYRROLO-[3,2-F]QUINAZOLINE-1,3-DIAMINE / GW345


Mass: 269.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H19N5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.27 Å3/Da / Density % sol: 43 %
Crystal growpH: 6.5
Details: A THREE-FOLD EXCESS OF GW345 AND THREE-FOLD EXCESS OF NADPH WAS ADDED TO THE C. ALBICANS DHFR SOLUTION AND LET STAND 277K OVERNIGHT. 17-20 MG/ML C. ALBICANS DHFR IN 50 UM GW345, 50 UM NADPH, ...Details: A THREE-FOLD EXCESS OF GW345 AND THREE-FOLD EXCESS OF NADPH WAS ADDED TO THE C. ALBICANS DHFR SOLUTION AND LET STAND 277K OVERNIGHT. 17-20 MG/ML C. ALBICANS DHFR IN 50 UM GW345, 50 UM NADPH, 20 MM KMES, 1 MM DTT, PH 6.5 WAS MIXED WITH AN EQUAL PART OF 26 - 34% PEG-3350, THE RESERVOIR SOLUTION.
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117-20 mg/mlprotein1drop
226-34 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 9, 1987 / Details: MONOCHROMATOR
RadiationMonochromator: HUBER MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.6 Å / Num. obs: 45668 / % possible obs: 91.7 % / Observed criterion σ(I): 2 / Redundancy: 3.06 % / Rsym value: 0.0458
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 1.59 % / Mean I/σ(I) obs: 3.06 / Rsym value: 0.235 / % possible all: 53
Reflection
*PLUS
Num. measured all: 139612 / Rmerge(I) obs: 0.0458
Reflection shell
*PLUS
% possible obs: 53 % / Rmerge(I) obs: 0.235

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Processing

Software
NameClassification
PROFFTrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: DIRECT REPLACEMENT
Starting model: CANDIDA ALBICANS DHFR (PDB ENTRY 1AI9)

1ai9


Resolution: 1.6→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.155 --
all-45668 -
obs-41400 91.7 %
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 0 136 353 3671
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.03
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1
X-RAY DIFFRACTIONp_mcbond_it4.61
X-RAY DIFFRACTIONp_mcangle_it5.5372
X-RAY DIFFRACTIONp_scbond_it7.7832.5
X-RAY DIFFRACTIONp_scangle_it9.4265
X-RAY DIFFRACTIONp_plane_restr0.020.03
X-RAY DIFFRACTIONp_chiral_restr0.2410.3
X-RAY DIFFRACTIONp_singtor_nbd0.1650.2
X-RAY DIFFRACTIONp_multtor_nbd0.1450.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2
X-RAY DIFFRACTIONp_xyhbond_nbd0.1270.2
X-RAY DIFFRACTIONp_planar_tor3.86
X-RAY DIFFRACTIONp_staggered_tor14.910
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor3110
X-RAY DIFFRACTIONp_special_tor6

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