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- PDB-9g4h: The structure of Candida albicans phosphoglucose isomerase in com... -

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Basic information

Entry
Database: PDB / ID: 9g4h
TitleThe structure of Candida albicans phosphoglucose isomerase in complex with fragments
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / PGI / Candida / fragment
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
: / 5-PHOSPHOARABINONIC ACID / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsYan, K.
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: Exploration of starting points for the chemical validation of UDP-N-acetylglucosamine pyrophosphorylase in Aspergillus fumigatus
Authors: Yan, K. / Stanley, M. / Raimi, O. / Kowalski, B. / Gurvic, D. / Grillenberger, S. / Chen, X. / Ferenbach, A.T. / Dorfmueller, H. / van Aalten, D.M.F.
History
DepositionJul 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 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
B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1856
Polymers123,3412
Non-polymers8444
Water15,997888
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13890 Å2
ΔGint-83 kcal/mol
Surface area35060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.088, 101.354, 135.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2
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-PA5 / 5-PHOSPHOARABINONIC ACID


Type: saccharide / Mass: 246.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11O9P
#3: Chemical ChemComp-A1IHU / 4-bromanyl-2-methyl-pyrazol-3-amine


Mass: 176.015 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6BrN3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 888 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MgCl2, 0.1 M Hepes-NaOH pH7.0, 21 % PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.529→81.173 Å / Num. obs: 153067 / % possible obs: 92.8 % / Redundancy: 11.1 % / CC1/2: 0.998 / Net I/σ(I): 7.2
Reflection shellResolution: 1.529→1.611 Å / Num. unique obs: 7653 / CC1/2: 0.956

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→73.27 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2746 7492 4.9 %
Rwork0.2507 --
obs0.2519 152833 84.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.53→73.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8610 0 46 888 9544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059000
X-RAY DIFFRACTIONf_angle_d0.79412243
X-RAY DIFFRACTIONf_dihedral_angle_d12.993220
X-RAY DIFFRACTIONf_chiral_restr0.0511368
X-RAY DIFFRACTIONf_plane_restr0.0061572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.550.3586530.3082898X-RAY DIFFRACTION16
1.55-1.560.3544650.28141302X-RAY DIFFRACTION23
1.56-1.580.3061910.26941782X-RAY DIFFRACTION31
1.58-1.60.28641090.26982303X-RAY DIFFRACTION41
1.6-1.630.29411360.25492962X-RAY DIFFRACTION52
1.63-1.650.25972060.24993523X-RAY DIFFRACTION62
1.65-1.670.29252220.24164045X-RAY DIFFRACTION71
1.67-1.70.30792290.23134527X-RAY DIFFRACTION80
1.7-1.720.26592660.23044860X-RAY DIFFRACTION86
1.72-1.750.27762320.22085081X-RAY DIFFRACTION89
1.75-1.780.25412770.21775202X-RAY DIFFRACTION91
1.78-1.810.23833020.21855383X-RAY DIFFRACTION95
1.81-1.850.2572920.21585593X-RAY DIFFRACTION98
1.85-1.890.23673030.2245662X-RAY DIFFRACTION100
1.89-1.930.23942910.22475634X-RAY DIFFRACTION99
1.93-1.970.27012840.2165728X-RAY DIFFRACTION100
1.97-2.020.24242640.21335760X-RAY DIFFRACTION100
2.02-2.080.27173030.20795666X-RAY DIFFRACTION99
2.08-2.140.25563160.21385686X-RAY DIFFRACTION100
2.14-2.210.24213120.21735714X-RAY DIFFRACTION100
2.21-2.280.2732930.22655666X-RAY DIFFRACTION99
2.28-2.380.24962750.23565783X-RAY DIFFRACTION100
2.38-2.480.28743080.24765728X-RAY DIFFRACTION100
2.48-2.620.2842730.26215762X-RAY DIFFRACTION100
2.62-2.780.30352960.27385759X-RAY DIFFRACTION100
2.78-2.990.28122770.28115787X-RAY DIFFRACTION100
2.99-3.290.30392990.28035796X-RAY DIFFRACTION100
3.29-3.770.27123170.26455793X-RAY DIFFRACTION100
3.77-4.750.25173050.26555877X-RAY DIFFRACTION100
4.75-73.270.33492960.32056079X-RAY DIFFRACTION99

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