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- PDB-4h97: Candida albicans dihydrofolate reductase complexed with NADPH and... -

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Basic information

Entry
Database: PDB / ID: 4h97
TitleCandida albicans dihydrofolate reductase complexed with NADPH and 5-{3-[3-methoxy-5-(4-methylphenyl)phenyl]but-1-yn-1-yl}-6-methylpyrimidine-2,4-diamine (UCP111D4M)
ComponentsDihydrofolate Reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Antifungal Agents / Candida albicans / Drug Design / Enzyme Inhibitors / Fungal Proteins / Tetrahydrofolate Dehydrogenase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


dihydrofolate metabolic process / folic acid metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / mitochondrion
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-53S / Chem-NDP / Dihydrofolate reductase / Dihydrofolate reductase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsPaulsen, J.L. / Anderson, A.C.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Structural analysis of the active sites of dihydrofolate reductase from two species of Candida uncovers ligand-induced conformational changes shared among species.
Authors: Paulsen, J.L. / Viswanathan, K. / Wright, D.L. / Anderson, A.C.
History
DepositionSep 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Non-polymer description
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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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)46,2287
Polymers43,9002
Non-polymers2,3285
Water37821
1
A: Dihydrofolate Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0683
Polymers21,9501
Non-polymers1,1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1604
Polymers21,9501
Non-polymers1,2103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.000, 118.000, 39.116
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Dihydrofolate Reductase


Mass: 21950.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: DFR1, DHFR / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5A5E0, UniProt: P22906*PLUS, 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: Chemical ChemComp-53S / 5-[(3R)-3-(5-methoxy-4'-methylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine


Mass: 372.463 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H24N4O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.1 Å3/Da / Density % sol: 60.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, KMES, glycine, pH 6.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.589
11K, H, -L20.411
ReflectionResolution: 2.2→25.1 Å / Num. all: 28587 / Num. obs: 28587 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.89 % / Rmerge(I) obs: 0.093 / Χ2: 2.06 / Net I/σ(I): 14 / Scaling rejects: 1488
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.2-2.287.050.5554.21988028181.58100
2.28-2.377.060.5074.61962727771.65100
2.37-2.487.080.4315.62010828361.84100
2.48-2.6170.3756.61992228352.09100
2.61-2.777.020.3267.91985928142.31100
2.77-2.986.270.3228.91794428303.03100
2.98-3.286.990.15515.52025328762.5999.8
3.28-3.766.890.09321.71986728382.2899.8
3.76-4.736.870.0628.82030829091.6199.7
4.73-25.16.640.05334.72054830541.7299.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.9.8.8Ldata reduction
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AOE

1aoe


Resolution: 2.2→25.1 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0 / SU B: 7.868 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2844 1420 5 %RANDOM
Rwork0.2639 ---
obs0.2643 28533 99.65 %-
all-28533 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.09 Å2 / Biso mean: 44.0152 Å2 / Biso min: 22.68 Å2
Baniso -1Baniso -2Baniso -3
1--3.85 Å20 Å20 Å2
2--5.3 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3088 0 158 21 3267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223332
X-RAY DIFFRACTIONr_angle_refined_deg1.1052.0274541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.4155380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.95224.085142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.16115584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9951522
X-RAY DIFFRACTIONr_chiral_restr0.0420.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212454
X-RAY DIFFRACTIONr_mcbond_it0.2921.51909
X-RAY DIFFRACTIONr_mcangle_it0.52823134
X-RAY DIFFRACTIONr_scbond_it0.43931423
X-RAY DIFFRACTIONr_scangle_it0.7834.51406
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 114 -
Rwork0.291 1915 -
all-2029 -
obs--98.64 %

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