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- PDB-9g07: The structure of Candida albicans phosphoglucose isomerase in com... -

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Basic information

Entry
Database: PDB / ID: 9g07
TitleThe structure of Candida albicans phosphoglucose isomerase in complex with a fragment
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: 1.66 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: Using a fragment-based approach to explore starting points for chemical validation of antimicrobial targets
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 7, 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)62,0933
Polymers61,6701
Non-polymers4222
Water7,873437
1
A: Glucose-6-phosphate isomerase
hetero molecules

A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1856
Polymers123,3412
Non-polymers8444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area13840 Å2
ΔGint-86 kcal/mol
Surface area35020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.100, 87.359, 101.309
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-957-

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: Chemical ChemComp-A1IHU / 4-bromanyl-2-methyl-pyrazol-3-amine


Mass: 176.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6BrN3 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-PA5 / 5-PHOSPHOARABINONIC ACID


Type: saccharide / Mass: 246.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 49.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MgCl2, 0.1 M Hepes-NaOH pH 7.0, 21 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.66→29.77 Å / Num. obs: 70609 / % possible obs: 98 % / Redundancy: 11.4 % / CC1/2: 0.997 / Net I/σ(I): 15.5
Reflection shellResolution: 1.66→1.69 Å / Num. unique obs: 2889 / CC1/2: 0.743

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→29.77 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.663 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18474 3628 5.1 %RANDOM
Rwork0.15978 ---
obs0.16109 66913 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.778 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å2-0 Å20 Å2
2---1.09 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: 1 / Resolution: 1.66→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4309 0 23 437 4769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124468
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164024
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.6446068
X-RAY DIFFRACTIONr_angle_other_deg0.6191.5679371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.264513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84710728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1030.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025065
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02912
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_it1.6541.6952215
X-RAY DIFFRACTIONr_mcbond_other1.6521.6952215
X-RAY DIFFRACTIONr_mcangle_it2.2932.5362770
X-RAY DIFFRACTIONr_mcangle_other2.2982.5382771
X-RAY DIFFRACTIONr_scbond_it2.7361.9142253
X-RAY DIFFRACTIONr_scbond_other2.7361.9142254
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9112.7623293
X-RAY DIFFRACTIONr_long_range_B_refined4.9125.7325235
X-RAY DIFFRACTIONr_long_range_B_other4.80824.3995130
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 224 -
Rwork0.297 4179 -
obs--83.8 %

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