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- PDB-7yva: Crystal structure of Candida albicans Fructose-1,6-bisphosphate a... -

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Basic information

Entry
Database: PDB / ID: 7yva
TitleCrystal structure of Candida albicans Fructose-1,6-bisphosphate aldolase complexed with lipoic acid
ComponentsCandida albicans Fructose-1,6-bisphosphate aldolase
KeywordsCYTOSOLIC PROTEIN/INHIBITOR / non-covalent inhibitor / CYTOSOLIC PROTEIN-INHIBITOR COMPLEX
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
LIPOIC ACID / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsCao, H. / Huang, Y. / Ren, Y. / Wan, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177036 China
CitationJournal: To Be Published
Title: Crystal structure of Candida albicans Fructose-1,6-bisphosphate aldolase complexed with lipoic acid
Authors: Cao, H. / Huang, Y. / Ren, Y. / Wan, J.
History
DepositionAug 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Candida albicans Fructose-1,6-bisphosphate aldolase
B: Candida albicans Fructose-1,6-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9887
Polymers78,5272
Non-polymers4615
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-59 kcal/mol
Surface area25080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.181, 56.622, 81.839
Angle α, β, γ (deg.)90.000, 96.330, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Candida albicans Fructose-1,6-bisphosphate aldolase


Mass: 39263.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9URB4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-LPA / LIPOIC ACID / 5-[(3R)-1,2-dithiolan-3-yl]pentanoic acid / Lipoic acid


Mass: 206.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 22.5% (w/v) PEG 3350 100 mM Hepes pH =7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.93→45.37 Å / Num. obs: 15544 / % possible obs: 98.47 % / Redundancy: 3.3 % / Biso Wilson estimate: 79.64 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.38
Reflection shellResolution: 2.93→3.04 Å / Num. unique obs: 1493 / CC1/2: 0.752

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LNK

6lnk


Resolution: 2.93→45.37 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 1553 10 %
Rwork0.2036 13983 -
obs0.209 15536 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.36 Å2 / Biso mean: 77.9798 Å2 / Biso min: 47.79 Å2
Refinement stepCycle: final / Resolution: 2.93→45.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5170 0 22 103 5295
Biso mean--75.28 78.96 -
Num. residues----672
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 (%)
2.93-3.030.40281370.3431227136497
3.03-3.140.40961370.31071244138197
3.14-3.260.32441430.27271277142099
3.26-3.410.25961390.250712631402100
3.41-3.590.31981420.25581272141499
3.59-3.820.30741400.19911270141099
3.82-4.110.24111390.18051255139498
4.11-4.520.20141430.17191281142499
4.52-5.170.20591410.16921280142199
5.18-6.520.28291440.20791288143298
6.52-45.370.22041480.17791326147498
Refinement TLS params.Method: refined / Origin x: -23.2191 Å / Origin y: 1.4468 Å / Origin z: 17.3697 Å
111213212223313233
T0.4184 Å20.1108 Å2-0.0315 Å2-0.426 Å2-0.1 Å2--0.5472 Å2
L1.0937 °20.3241 °2-0.8085 °2-0.6809 °2-1.048 °2--5.5623 °2
S0.0409 Å °0.0966 Å °0.1903 Å °0.1989 Å °0.0062 Å °0.1431 Å °-0.4946 Å °-0.6588 Å °-0.0513 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 401
2X-RAY DIFFRACTION1allB2 - 401
3X-RAY DIFFRACTION1allB501 - 503
4X-RAY DIFFRACTION1allS1 - 108

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