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- PDB-1ai9: CANDIDA ALBICANS DIHYDROFOLATE REDUCTASE -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1ai9
TitleCANDIDA ALBICANS DIHYDROFOLATE REDUCTASE
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / ANTIFUNGAL TARGET / REDUCTASE
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, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 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.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
DepositionMay 1, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,8804
Polymers44,3892
Non-polymers1,4912
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.200, 67.570, 38.660
Angle α, β, γ (deg.)90.00, 93.06, 90.00
Int Tables number4
Space group name H-MP1211

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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
Details: ACTS AS A MONOMER WITH NADPH / Source: (gene. exp.) Candida albicans (yeast) / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P22906, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: 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: 2.27 Å3/Da / Density % sol: 43 %
Crystal growpH: 7.5
Details: 17-20 MG/ML C. ALBICANS DHFR IN 20 MM KMES, 1 MM DTT, 0.1 MM EDTA, 20% GLYERCOL, PH 7.5 WAS MIXED WITH AN EQUAL PART OF 26 - 34% PEG-3350, THE RESERVOIR SOLUTION.
Crystal
*PLUS
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: May 1, 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: 1.83 Å / Num. obs: 31520 / % possible obs: 90.3 % / Observed criterion σ(I): 2 / Redundancy: 4.46 % / Rsym value: 0.0664 / Net I/σ(I): 16.9
Reflection shellResolution: 1.83→1.95 Å / Redundancy: 2.26 % / Mean I/σ(I) obs: 3.11 / Rsym value: 0.3535 / % possible all: 83.5
Reflection
*PLUS
Num. measured all: 140620 / Rmerge(I) obs: 0.0704

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Processing

Software
NameClassification
MERLOTphasing
PROFFTrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MURINE DHFR

Resolution: 1.85→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.199 --
all-31520 -
obs-28540 90 %
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 96 160 3452
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0250.03
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9131
X-RAY DIFFRACTIONp_mcangle_it1.512
X-RAY DIFFRACTIONp_scbond_it1.6381.5
X-RAY DIFFRACTIONp_scangle_it2.5883
X-RAY DIFFRACTIONp_plane_restr0.0220.03
X-RAY DIFFRACTIONp_chiral_restr0.2940.3
X-RAY DIFFRACTIONp_singtor_nbd0.1720.2
X-RAY DIFFRACTIONp_multtor_nbd0.1610.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2
X-RAY DIFFRACTIONp_xyhbond_nbd0.1430.2
X-RAY DIFFRACTIONp_planar_tor4.66
X-RAY DIFFRACTIONp_staggered_tor17.610
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.410
X-RAY DIFFRACTIONp_special_tor6
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS

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