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- PDB-9g46: The structure of Candida albicans phosphoglucose isomerae (CaPGI)... -

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Basic information

Entry
Database: PDB / ID: 9g46
TitleThe structure of Candida albicans phosphoglucose isomerae (CaPGI) 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: 1.44 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

Downloads & links

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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)124,53510
Polymers123,3412
Non-polymers1,1948
Water19,9611108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14810 Å2
ΔGint-107 kcal/mol
Surface area34990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.769, 101.170, 133.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#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

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Non-polymers , 4 types, 1114 molecules

#3: Chemical ChemComp-A1IIA / (1S)-3-(methylamino)-1-thiophen-2-yl-propan-1-ol


Mass: 171.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NOS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1IH8 / [4-(hydroxymethyl)cyclohexyl]methanol


Mass: 144.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1108 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.3 %
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: 1.44→29.82 Å / Num. obs: 171681 / % possible obs: 80.2 % / Redundancy: 9.9 % / CC1/2: 0.999 / Net I/σ(I): 17.8
Reflection shellResolution: 1.44→1.46 Å / Num. unique obs: 831 / CC1/2: 0.449

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→29.82 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.11 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17904 8496 5 %RANDOM
Rwork0.1546 ---
obs0.15581 163077 80.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.281 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å2-0 Å2
2---0.46 Å20 Å2
3---1 Å2
Refinement stepCycle: 1 / Resolution: 1.44→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8597 0 74 1108 9779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0128995
X-RAY DIFFRACTIONr_bond_other_d0.0020.0168134
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.64612226
X-RAY DIFFRACTIONr_angle_other_deg0.641.57718971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50951141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.81524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.092101472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.21368
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021826
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_it1.2471.2084442
X-RAY DIFFRACTIONr_mcbond_other1.2471.2084442
X-RAY DIFFRACTIONr_mcangle_it1.811.815560
X-RAY DIFFRACTIONr_mcangle_other1.8111.8115561
X-RAY DIFFRACTIONr_scbond_it2.2891.4034553
X-RAY DIFFRACTIONr_scbond_other2.2891.4034554
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3612.0166645
X-RAY DIFFRACTIONr_long_range_B_refined4.39818.59410652
X-RAY DIFFRACTIONr_long_range_B_other4.17716.00310327
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.44→1.475 Å
RfactorNum. reflection% reflection
Rfree0.354 90 -
Rwork0.339 1805 -
obs--12.14 %

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