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

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Basic information

Entry
Database: PDB / ID: 8crh
TitleCrystal structure of Candida auris dihydrofolate reductase complexed with NADPH and cycloguanil
ComponentsDihydrofolate reductase
KeywordsHYDROLASE / Dihydrofolate reductase candida auris NADPH cycloguanil
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, 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-NDP / Chem-VIL / Dihydrofolate reductase
Similarity search - Component
Biological species[Candida] auris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKirkman, T.J. / Dias, M.V.B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI) United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Crystal structure of dihydrofolate reductase from the emerging pathogenic fungus Candida auris.
Authors: Kirkman, T. / Sketcher, A. / de Morais Barroso, V. / Ishida, K. / Tosin, M. / Dias, M.V.B.
History
DepositionMar 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,08113
Polymers48,0952
Non-polymers2,98611
Water11,223623
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-68 kcal/mol
Surface area21030 Å2
Unit cell
Length a, b, c (Å)43.776, 63.624, 167.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dihydrofolate reductase


Mass: 24047.609 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 BL21(DE3) (bacteria) / References: UniProt: A0A0L0P1H8
#2: Chemical
ChemComp-VIL / 5-(4-chlorophenyl)-6,6-dimethyl-1,4-dihydro-1,3,5-triazine-2,4-diamine


Mass: 253.731 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H16ClN5 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M Lithium sulphate, 0.1 M Tris, 27.5% 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 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→42.36 Å / Num. obs: 112746 / % possible obs: 96.97 % / Redundancy: 11.6 % / Biso Wilson estimate: 16.11 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.01397 / Rrim(I) all: 0.05006 / Net I/σ(I): 19.59
Reflection shellResolution: 1.3→1.346 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.4086 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 9094 / CC1/2: 0.907 / CC star: 0.975 / Rpim(I) all: 0.2003 / Rrim(I) all: 0.458 / % possible all: 79.51

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.18.2_3874refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→42.36 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.183 1995 1.77 %
Rwork0.1734 --
obs0.1736 112516 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3331 0 189 623 4143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083670
X-RAY DIFFRACTIONf_angle_d1.414995
X-RAY DIFFRACTIONf_dihedral_angle_d19.196496
X-RAY DIFFRACTIONf_chiral_restr0.112519
X-RAY DIFFRACTIONf_plane_restr0.007616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.33881110.33266245X-RAY DIFFRACTION77
1.33-1.370.31651250.2916925X-RAY DIFFRACTION86
1.37-1.410.27921390.26297647X-RAY DIFFRACTION95
1.41-1.450.22921430.2237935X-RAY DIFFRACTION99
1.45-1.510.20291450.20158050X-RAY DIFFRACTION100
1.51-1.570.18341460.198077X-RAY DIFFRACTION100
1.57-1.640.19991460.18448074X-RAY DIFFRACTION100
1.64-1.720.20451460.17568094X-RAY DIFFRACTION100
1.72-1.830.19681470.17888108X-RAY DIFFRACTION100
1.83-1.970.18491470.17448135X-RAY DIFFRACTION100
1.97-2.170.19791470.16758163X-RAY DIFFRACTION100
2.17-2.490.17311490.17228195X-RAY DIFFRACTION100
2.49-3.130.18811490.17278294X-RAY DIFFRACTION100
3.13-42.360.14751550.14628579X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -16.6136 Å / Origin y: 10.4312 Å / Origin z: 52.5382 Å
111213212223313233
T0.1045 Å20.0049 Å2-0.0006 Å2-0.1168 Å20.0019 Å2--0.1569 Å2
L0.1781 °20.034 °20.2129 °2-0.3504 °20.3278 °2--1.4664 °2
S0.0048 Å °0.0109 Å °-0.0158 Å °0.0119 Å °0.0004 Å °-0.0143 Å °0.0035 Å °0.0918 Å °-0.0053 Å °
Refinement TLS groupSelection details: all

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