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- PDB-9g47: The structure of Candida albicans phosphoglucose isomerase in com... -

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Basic information

Entry
Database: PDB / ID: 9g47
TitleThe structure of Candida albicans phosphoglucose isomerase in complex with a fragment binder
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: 1.51 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 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 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)124,1256
Polymers123,3412
Non-polymers7854
Water19,5461085
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13470 Å2
ΔGint-82 kcal/mol
Surface area34990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.777, 101.212, 135.322
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-A1IIC / quinoxalin-5-ol


Mass: 146.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1085 / 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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MgCl2, 0.1 M Hepes-NaOH pH 7.0, 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: 1.506→81.05 Å / Num. obs: 154412 / % possible obs: 84.2 % / Redundancy: 11.4 % / CC1/2: 1 / Net I/σ(I): 19.6
Reflection shellResolution: 1.506→1.569 Å / Num. unique obs: 7721 / CC1/2: 0.983

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→81.05 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 44.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 7724 5.01 %
Rwork0.2114 --
obs0.2122 154083 81.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→81.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8607 0 52 1085 9744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058991
X-RAY DIFFRACTIONf_angle_d0.78712231
X-RAY DIFFRACTIONf_dihedral_angle_d12.6843205
X-RAY DIFFRACTIONf_chiral_restr0.0521364
X-RAY DIFFRACTIONf_plane_restr0.0061572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.520.34321060.31161796X-RAY DIFFRACTION31
1.52-1.540.32651040.30082071X-RAY DIFFRACTION35
1.54-1.560.31071000.28062348X-RAY DIFFRACTION39
1.56-1.580.27051370.27072568X-RAY DIFFRACTION43
1.58-1.60.28851630.25852805X-RAY DIFFRACTION48
1.6-1.620.25841810.24823105X-RAY DIFFRACTION53
1.62-1.650.25551840.23593364X-RAY DIFFRACTION57
1.65-1.670.22261780.23153695X-RAY DIFFRACTION62
1.67-1.70.26982000.21763967X-RAY DIFFRACTION67
1.7-1.720.25782370.21864243X-RAY DIFFRACTION72
1.72-1.750.2552850.21464577X-RAY DIFFRACTION78
1.75-1.790.21132790.21184924X-RAY DIFFRACTION84
1.79-1.820.20422700.20775368X-RAY DIFFRACTION90
1.82-1.860.23192810.20355841X-RAY DIFFRACTION98
1.86-1.90.21982990.20265915X-RAY DIFFRACTION100
1.9-1.940.19743270.18955884X-RAY DIFFRACTION100
1.94-1.990.20733560.17865904X-RAY DIFFRACTION100
1.99-2.040.21263010.1765893X-RAY DIFFRACTION100
2.04-2.10.19493160.17455922X-RAY DIFFRACTION100
2.1-2.170.18633380.17685931X-RAY DIFFRACTION100
2.17-2.250.20833080.18025955X-RAY DIFFRACTION100
2.25-2.340.20623180.18625955X-RAY DIFFRACTION100
2.34-2.450.21123070.18985954X-RAY DIFFRACTION100
2.45-2.580.2272930.20695979X-RAY DIFFRACTION100
2.58-2.740.22113000.21916018X-RAY DIFFRACTION100
2.74-2.950.25752750.23125995X-RAY DIFFRACTION100
2.95-3.240.24493010.22186051X-RAY DIFFRACTION100
3.24-3.710.2163180.21346047X-RAY DIFFRACTION100
3.71-4.680.20833290.20526064X-RAY DIFFRACTION100
4.68-81.050.26793330.26336220X-RAY DIFFRACTION98

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