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- PDB-7v6f: Structure of Candida albicans Fructose-1,6-bisphosphate aldolase ... -

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Basic information

Entry
Database: PDB / ID: 7v6f
TitleStructure of Candida albicans Fructose-1,6-bisphosphate aldolase complexed with G3P
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / FBA
Function / homology
Function and homology information


: / 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 ...: / 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
GLYCERALDEHYDE-3-PHOSPHATE / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsHongxuan, C. / Huang, Y. / Han, C. / Chen, W. / 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
DepositionAug 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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)80,4855
Polymers80,1842
Non-polymers3013
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-72 kcal/mol
Surface area25620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.458, 56.570, 131.747
Angle α, β, γ (deg.)90.000, 113.430, 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-G3H / GLYCERALDEHYDE-3-PHOSPHATE / Glyceraldehyde 3-phosphate


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / 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: Jan 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.885→43.68 Å / Num. obs: 18393 / % possible obs: 99.49 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 22.7
Reflection shellResolution: 2.885→2.988 Å / CC1/2: 0.999

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LNK

6lnk


Resolution: 2.98→43.68 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.91 / SU B: 27.549 / SU ML: 0.472 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.487 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28 833 5 %RANDOM
Rwork0.2172 ---
obs0.2204 15822 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 164.63 Å2 / Biso mean: 55.607 Å2 / Biso min: 12.56 Å2
Baniso -1Baniso -2Baniso -3
1-11.18 Å2-0 Å2-6.19 Å2
2---0.28 Å2-0 Å2
3----4.02 Å2
Refinement stepCycle: final / Resolution: 2.98→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5142 0 12 15 5169
Biso mean--87.42 28.17 -
Num. residues----672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125273
X-RAY DIFFRACTIONr_angle_refined_deg1.491.6347141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9275666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27123.884242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.70415863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1821516
X-RAY DIFFRACTIONr_chiral_restr0.1190.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023998
LS refinement shellResolution: 2.984→3.062 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 58 -
Rwork0.394 1113 -
all-1171 -
obs--98.32 %

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