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- PDB-8a0z: Crystal structure of Candida auris dihydrofolate reductase comple... -

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Basic information

Entry
Database: PDB / ID: 8a0z
TitleCrystal structure of Candida auris dihydrofolate reductase complexed with NADPH and pyrimethamine
ComponentsDihydrofolate reductase
KeywordsHYDROLASE / Dihydrofolate reductase candida auris NADPH pyrimethamine
Function / homology
Function and homology information


dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / mitochondrion / cytosol
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-CP6 / Chem-NDP / NITRATE ION / Dihydrofolate reductase
Similarity search - Component
Biological species[Candida] auris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKirkman, T.K. / Dias, M.V.B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI) United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of candida auris
Authors: Kirkman, T.K. / Dias, M.V.B.
History
DepositionMay 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Dihydrofolate reductase
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,85710
Polymers47,2682
Non-polymers2,5898
Water6,413356
1
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9295
Polymers23,6341
Non-polymers1,2944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9295
Polymers23,6341
Non-polymers1,2944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.179, 45.449, 54.074
Angle α, β, γ (deg.)105.270, 93.330, 90.200
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Dihydrofolate reductase


Mass: 23634.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Candida] auris (fungus) / Gene: QG37_02791 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L0P1H8, dihydrofolate reductase

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Non-polymers , 5 types, 364 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CP6 / 5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE / PYRIMETHAMINE


Mass: 248.711 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13ClN4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antiparasitic*YM
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium nitrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→51.98 Å / Num. obs: 34623 / % possible obs: 83.2 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.031 / Rrim(I) all: 0.059 / Net I/σ(I): 11.9 / Num. measured all: 121303 / Scaling rejects: 172
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.7330.23520887000.9440.1560.283431.9
8.98-51.983.80.02210332740.9990.0130.02621.198.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZZX

7zzx


Resolution: 1.7→41.1 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 1995 5.77 %
Rwork0.1901 32583 -
obs0.192 34578 83.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.33 Å2 / Biso mean: 22.1853 Å2 / Biso min: 8.24 Å2
Refinement stepCycle: final / Resolution: 1.7→41.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 185 356 3837
Biso mean--22.85 29.43 -
Num. residues----404
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.740.2647610.2313951101234
1.74-1.790.2537740.23831148122241
1.79-1.840.2777890.22951467155653
1.84-1.90.25961070.21861829193666
1.9-1.970.24521460.19792574272091
1.97-2.050.24261730.20182682285596
2.05-2.140.25241560.20232703285997
2.14-2.250.25981740.19482724289897
2.25-2.40.21771650.19962722288798
2.4-2.580.25511700.20812754292498
2.58-2.840.25331640.20692745290998
2.84-3.250.22471700.19232759292999
3.25-4.090.17891760.16792768294499
4.1-41.10.19841700.16952757292799

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