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- PDB-7zzx: Crystal structure of Candida auris DHFR in apo form -

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Basic information

Entry
Database: PDB / ID: 7zzx
TitleCrystal structure of Candida auris DHFR in apo form
ComponentsDihydrofolate reductase
KeywordsHYDROLASE / Dihydrofolate reductase Candida auris
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
Dihydrofolate reductase
Similarity search - Component
Biological species[Candida] auris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionMay 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Aug 9, 2023Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Feb 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

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Assembly

Deposited unit
B: Dihydrofolate reductase


Theoretical massNumber of molelcules
Total (without water)23,6341
Polymers23,6341
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.300, 146.300, 31.514
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Dihydrofolate reductase


Mass: 23634.137 Da / Num. of mol.: 1
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 4.12 Å3/Da / Density % sol: 70.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Sodium citrate 1.6 M, pH = 6.3

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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: Mar 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→73.16 Å / Num. obs: 15293 / % possible obs: 99.9 % / Redundancy: 19.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.041 / Rrim(I) all: 0.182 / Net I/σ(I): 12.8 / Num. measured all: 300922 / Scaling rejects: 111
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
2.4-2.4916.82.1682655215820.7510.5462.2371.898.7
8.99-73.1618.20.051599733010.0120.05336.599.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AOE

1aoe


Resolution: 2.4→42.23 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2305 1525 9.99 %
Rwork0.205 13738 -
obs0.2075 15263 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.99 Å2 / Biso mean: 69.3371 Å2 / Biso min: 36.81 Å2
Refinement stepCycle: final / Resolution: 2.4→42.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 0 41 1677
Biso mean---57.02 -
Num. residues----202
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.480.33981340.29441221135599
2.48-2.570.31521410.281112411382100
2.57-2.670.27871380.27412501388100
2.67-2.790.29161350.251612191354100
2.79-2.940.26231390.239212481387100
2.94-3.120.26281410.24712441385100
3.12-3.360.30451350.221812291364100
3.36-3.70.22381440.192412531397100
3.7-4.240.21881330.176612541387100
4.24-5.330.17511410.16812811422100
5.34-42.230.20861440.200812981442100
Refinement TLS params.Method: refined / Origin x: 67.324 Å / Origin y: -18.8506 Å / Origin z: 14.3894 Å
111213212223313233
T0.5149 Å2-0.0042 Å2-0.024 Å2-0.3514 Å2-0.0133 Å2--0.4396 Å2
L0.5406 °20.0523 °2-0.1339 °2-1.3911 °2-0.9145 °2--1.319 °2
S0.039 Å °0.008 Å °-0.025 Å °0.1073 Å °0.0167 Å °0.2128 Å °-0.2038 Å °-0.0169 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB2 - 203
2X-RAY DIFFRACTION1allS1 - 43

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