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- PDB-9fzt: The structure of Candida albicans phosphoglucose isomerase in com... -

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Basic information

Entry
Database: PDB / ID: 9fzt
TitleThe structure of Candida albicans phosphoglucose isomerase in complex with fructose-6-phosphate
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / PGI / Candida
Function / homology
Function and homology information


fungal biofilm matrix / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / monosaccharide binding / gluconeogenesis / glycolytic process / mitochondrion / cytosol
Similarity search - Function
Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / SIS domain superfamily
Similarity search - Domain/homology
6-O-phosphono-beta-D-fructofuranose / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsYan, K. / Raimi, O.G. / Grillenberger, S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V001094/1 United Kingdom
Wellcome Trust200208 United Kingdom
CitationJournal: To Be Published
Title: Using a fragment-based approach to explore starting points for chemical tools that modulate the microbial cell wall
Authors: Yan, K. / Stanley, M. / Raimi, O.G. / Kowalski, B. / Gurvic, D. / Grillenberger, S. / Chen, X. / Ferenbach, A.T. / Dorfmueller, H. / van Aalten, D.M.F.
History
DepositionJul 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9663
Polymers61,6701
Non-polymers2962
Water8,629479
1
A: Glucose-6-phosphate isomerase
hetero molecules

A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,9326
Polymers123,3412
Non-polymers5914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area13690 Å2
ΔGint-93 kcal/mol
Surface area34500 Å2
Unit cell
Length a, b, c (Å)68.080, 87.360, 100.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-960-

HOH

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Components

#1: Protein Glucose-6-phosphate isomerase / GPI / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI


Mass: 61670.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: PGI1, CAALFM_CR06340CA, CaO19.11369, CaO19.3888 / Production host: Escherichia coli (E. coli) / References: UniProt: P83780, glucose-6-phosphate isomerase
#2: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 49.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MgCl2, 0.1 M Hepes-NaOH pH 7.0, 15 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→25.2 Å / Num. obs: 36501 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.989 / Net I/σ(I): 10
Reflection shellResolution: 2.09→2.14 Å / Num. unique obs: 2806 / CC1/2: 0.878

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→23.92 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.901 / SU B: 4.01 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20891 1811 5 %RANDOM
Rwork0.16793 ---
obs0.16998 34648 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.612 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20 Å2
2---0.04 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.09→23.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4285 0 17 479 4781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124429
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163950
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.6416022
X-RAY DIFFRACTIONr_angle_other_deg0.5271.5629190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4275559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.474513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6110686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025033
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02907
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6240.8862209
X-RAY DIFFRACTIONr_mcbond_other0.6240.8862209
X-RAY DIFFRACTIONr_mcangle_it1.0061.3252762
X-RAY DIFFRACTIONr_mcangle_other1.0071.3262763
X-RAY DIFFRACTIONr_scbond_it1.1810.9742220
X-RAY DIFFRACTIONr_scbond_other1.180.9742217
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7631.4173256
X-RAY DIFFRACTIONr_long_range_B_refined3.25415.0175307
X-RAY DIFFRACTIONr_long_range_B_other2.93613.4825154
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.14 Å
RfactorNum. reflection% reflection
Rfree0.238 115 -
Rwork0.173 2542 -
obs--100 %

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