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- PDB-9fkc: Crystal structure of human Glucose-6-phosphate isomerase with cit... -

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Basic information

Entry
Database: PDB / ID: 9fkc
TitleCrystal structure of human Glucose-6-phosphate isomerase with citraconate ligand
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / Metabolic regulation / glycolysis / modular inhibition
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis / Glycolysis ...glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis / Glycolysis / erythrocyte homeostasis / positive regulation of immunoglobulin production / ciliary membrane / response to testosterone / response to immobilization stress / humoral immune response / mesoderm formation / response to cadmium ion / response to muscle stretch / positive regulation of endothelial cell migration / response to progesterone / cytokine activity / glycolytic process / gluconeogenesis / TP53 Regulates Metabolic Genes / growth factor activity / response to estradiol / glucose homeostasis / secretory granule lumen / in utero embryonic development / ficolin-1-rich granule lumen / carbohydrate metabolic process / learning or memory / ubiquitin protein ligase binding / Neutrophil degranulation / negative regulation of apoptotic process / extracellular exosome / extracellular region / membrane / 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
BETA-MERCAPTOETHANOL / (~{Z})-2-methylbut-2-enedioic acid / TRIETHYLENE GLYCOL / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJonatansdottir, Y.Y. / Hjorleifsson, G.J.
Funding support Iceland, 2items
OrganizationGrant numberCountry
Other private2023
Other government239695-052 Iceland
CitationJournal: Febs J. / Year: 2025
Title: Human glycolysis isomerases are inhibited by weak metabolite modulators.
Authors: Jonatansdottir, Y.Y. / Rolfsson, O. / Hjorleifsson, J.G.
History
DepositionJun 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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
C: Glucose-6-phosphate isomerase
D: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,48914
Polymers252,9204
Non-polymers1,57010
Water31,4361745
1
A: Glucose-6-phosphate isomerase
D: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,3037
Polymers126,4602
Non-polymers8435
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14670 Å2
ΔGint-58 kcal/mol
Surface area35850 Å2
MethodPISA
2
B: Glucose-6-phosphate isomerase
C: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,1877
Polymers126,4602
Non-polymers7275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14200 Å2
ΔGint-65 kcal/mol
Surface area36010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.723, 107.838, 271.481
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glucose-6-phosphate isomerase / GPI / Autocrine motility factor / AMF / Neuroleukin / NLK / Phosphoglucose isomerase / PGI / ...GPI / Autocrine motility factor / AMF / Neuroleukin / NLK / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI / Sperm antigen 36 / SA-36


Mass: 63229.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPI / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: P06744, glucose-6-phosphate isomerase

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Non-polymers , 6 types, 1755 molecules

#2: Chemical
ChemComp-CIZ / (~{Z})-2-methylbut-2-enedioic acid / CITRACONATE


Mass: 130.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1745 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein buffer: 20 mM Tris pH 7.4, 30 mM NaCl, 20 mM citraconate ligand. Reservoir: 21% w/v PEG3500, 0.16 M CaCl2, and 0.058 M HEPES, pH 7.0 Co-crystallization with ligand: Hanging drop: 1.5: ...Details: Protein buffer: 20 mM Tris pH 7.4, 30 mM NaCl, 20 mM citraconate ligand. Reservoir: 21% w/v PEG3500, 0.16 M CaCl2, and 0.058 M HEPES, pH 7.0 Co-crystallization with ligand: Hanging drop: 1.5:0.5:1.5 ul - Protein (8 mg/ml):Seed stock:Reservoir. Cryoprotectant = a mixture containing the mother liquor, 24% v/v glycerol, and 15-20 mM ligand.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.6→46.32 Å / Num. obs: 310523 / % possible obs: 99.67 % / Redundancy: 9.1 % / Biso Wilson estimate: 21.02 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1769 / Rpim(I) all: 0.06094 / Rrim(I) all: 0.1873 / Net I/σ(I): 8.66
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 9.2 % / Rmerge(I) obs: 3.608 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 30661 / CC1/2: 0.464 / CC star: 0.796 / Rpim(I) all: 1.232 / Rrim(I) all: 3.816 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→46.32 Å / SU ML: 0.2238 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.2535
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2272 15571 5.02 %
Rwork0.1979 294565 -
obs0.1993 310136 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.96 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17734 0 105 1745 19584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006118261
X-RAY DIFFRACTIONf_angle_d0.771524693
X-RAY DIFFRACTIONf_chiral_restr0.04822672
X-RAY DIFFRACTIONf_plane_restr0.00883186
X-RAY DIFFRACTIONf_dihedral_angle_d9.68132442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.39765160.39969660X-RAY DIFFRACTION98.56
1.62-1.640.40785290.38669646X-RAY DIFFRACTION99.31
1.64-1.660.40445170.37799713X-RAY DIFFRACTION99.44
1.66-1.680.38824990.35089735X-RAY DIFFRACTION99.51
1.68-1.70.36785060.34739701X-RAY DIFFRACTION99.51
1.7-1.720.3655590.34229701X-RAY DIFFRACTION99.6
1.72-1.750.3445200.31489757X-RAY DIFFRACTION99.63
1.75-1.770.31744930.30119725X-RAY DIFFRACTION99.65
1.77-1.80.30935140.299744X-RAY DIFFRACTION99.62
1.8-1.830.32855020.28269780X-RAY DIFFRACTION99.71
1.83-1.860.30235390.26579701X-RAY DIFFRACTION99.71
1.86-1.90.28675450.2579731X-RAY DIFFRACTION99.6
1.9-1.930.26735050.24199765X-RAY DIFFRACTION99.57
1.93-1.970.26365030.23129774X-RAY DIFFRACTION99.63
1.97-2.020.25425370.22179778X-RAY DIFFRACTION99.85
2.02-2.060.24915050.21329800X-RAY DIFFRACTION99.86
2.06-2.110.24065170.20649820X-RAY DIFFRACTION99.79
2.11-2.170.23745270.19759758X-RAY DIFFRACTION99.8
2.17-2.240.23745320.19739824X-RAY DIFFRACTION99.88
2.24-2.310.22595110.18439822X-RAY DIFFRACTION99.85
2.31-2.390.2095250.18019810X-RAY DIFFRACTION99.86
2.39-2.490.2125430.17499819X-RAY DIFFRACTION99.86
2.49-2.60.22935260.1799866X-RAY DIFFRACTION99.9
2.6-2.740.24770.17269907X-RAY DIFFRACTION99.9
2.74-2.910.2055210.17539881X-RAY DIFFRACTION99.86
2.91-3.130.18975320.17079906X-RAY DIFFRACTION99.86
3.13-3.450.18185010.16559977X-RAY DIFFRACTION99.9
3.45-3.950.18925130.158410008X-RAY DIFFRACTION99.91
3.95-4.970.17015380.145310078X-RAY DIFFRACTION99.84
4.97-46.320.2195190.193110378X-RAY DIFFRACTION99.26

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