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- PDB-6lnk: Candida albicans Fructose-1,6-bisphosphate aldolase -

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Basic information

Entry
Database: PDB / ID: 6lnk
TitleCandida albicans Fructose-1,6-bisphosphate aldolase
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / aldolase
Function / homology
Function and homology information


symbiont-mediated perturbation of host immune response / hyphal cell wall / fungal-type cell wall / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / biological process involved in interaction with host / gluconeogenesis / glycolytic process / cell surface / zinc ion binding ...symbiont-mediated perturbation of host immune response / hyphal cell wall / fungal-type cell wall / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / biological process involved in interaction with host / gluconeogenesis / glycolytic process / cell surface / zinc ion binding / plasma membrane / cytosol
Similarity search - Function
Fructose-bisphosphate aldolase, class II, yeast/E. coli subtype / Fructose-bisphosphate aldolase class-II signature 1. / Fructose-bisphosphate aldolase class-II signature 2. / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / Aldolase-type TIM barrel
Similarity search - Domain/homology
Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.639 Å
AuthorsHuang, Y. / Cao, H. / Ren, Y. / Wan, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Med.Chem. / Year: 2022
Title: Structure-Guided Discovery of the Novel Covalent Allosteric Site and Covalent Inhibitors of Fructose-1,6-Bisphosphate Aldolase to Overcome the Azole Resistance of Candidiasis.
Authors: Wen, W. / Cao, H. / Huang, Y. / Tu, J. / Wan, C. / Wan, J. / Han, X. / Chen, H. / Liu, J. / Rao, L. / Su, C. / Peng, C. / Sheng, C. / Ren, Y.
History
DepositionDec 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: 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
A: Fructose-bisphosphate aldolase
B: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4396
Polymers80,1842
Non-polymers2554
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-64 kcal/mol
Surface area25220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.475, 56.758, 82.388
Angle α, β, γ (deg.)90.000, 95.850, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Fructose-bisphosphate aldolase / FBPA / 37 kDa major allergen / Fructose-1 / 6-bisphosphate aldolase / IgE-binding allergen


Mass: 40092.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Strain: SC5314 / Gene: FBA1, CAALFM_C401750CA, CaO19.12088, CaO19.4618 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9URB4, fructose-bisphosphate aldolase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM Hepes pH =7.5, 11% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.639→39.91 Å / Num. obs: 21939 / % possible obs: 98.2 % / Redundancy: 3.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.05
Reflection shellResolution: 2.639→2.652 Å / Rmerge(I) obs: 0.5715 / Num. unique obs: 1179

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B57

1b57


Resolution: 2.639→39.91 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.84
RfactorNum. reflection% reflection
Rfree0.2591 1098 5 %
Rwork0.1979 --
obs0.2011 21939 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.58 Å2 / Biso mean: 59.4305 Å2 / Biso min: 30.69 Å2
Refinement stepCycle: final / Resolution: 2.639→39.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5174 0 10 58 5242
Biso mean--51.05 59.93 -
Num. residues----673
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6391-2.75920.35541350.2628255899
2.7592-2.90460.31921350.24162568100
2.9046-3.08660.29881370.232593100
3.0866-3.32480.30281370.22572613100
3.3248-3.65910.28781360.20962586100
3.6591-4.18810.25121380.18112609100
4.1881-5.27470.22451380.17272632100
5.2747-39.910.22531420.18682682100

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