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- PDB-9fhf: Crystal structure of human Glucose-6-phosphate isomerase with dih... -

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Basic information

Entry
Database: PDB / ID: 9fhf
TitleCrystal structure of human Glucose-6-phosphate isomerase with dihydroxyacetone phosphate 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
1,3-DIHYDROXYACETONEPHOSPHATE / DI(HYDROXYETHYL)ETHER / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionMay 27, 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

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Assembly

Deposited unit
D: Glucose-6-phosphate isomerase
A: Glucose-6-phosphate isomerase
C: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,02512
Polymers252,9204
Non-polymers1,1058
Water15,745874
1
D: Glucose-6-phosphate isomerase
A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,0126
Polymers126,4602
Non-polymers5524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14180 Å2
ΔGint-67 kcal/mol
Surface area36020 Å2
MethodPISA
2
C: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,0126
Polymers126,4602
Non-polymers5524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14070 Å2
ΔGint-64 kcal/mol
Surface area36080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.676, 108.313, 271.497
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

#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
#2: Chemical
ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 874 / 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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein buffer: 20 mM Tris pH 7.4, 30 mM NaCl, 20 dihydroxyacetone phosphate ligand. Reservoir: 21% w/v PEG3500, 0.16 M CaCl2, and 0.058 M HEPES, pH 7.0 Co-crystallization with ligand: ...Details: Protein buffer: 20 mM Tris pH 7.4, 30 mM NaCl, 20 dihydroxyacetone phosphate 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.
Temp details: RT

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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: Oct 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→45.05 Å / Num. obs: 220113 / % possible obs: 99.87 % / Redundancy: 13.5 % / Biso Wilson estimate: 21.88 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.2689 / Rpim(I) all: 0.07588 / Rrim(I) all: 0.2796 / Net I/σ(I): 9.74
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 13.7 % / Rmerge(I) obs: 3.017 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 21752 / CC1/2: 0.695 / CC star: 0.906 / Rpim(I) all: 0.8364 / Rrim(I) all: 3.133 / % possible all: 99.91

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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: 1.8→45.05 Å / SU ML: 0.2205 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.1598
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2276 11027 5.01 %
Rwork0.1857 208885 -
obs0.1878 219912 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.66 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17684 0 68 874 18626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010618185
X-RAY DIFFRACTIONf_angle_d1.092424611
X-RAY DIFFRACTIONf_chiral_restr0.05752665
X-RAY DIFFRACTIONf_plane_restr0.01323172
X-RAY DIFFRACTIONf_dihedral_angle_d7.3722420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.37463400.33696870X-RAY DIFFRACTION99.94
1.82-1.840.33743430.3166940X-RAY DIFFRACTION99.88
1.84-1.860.33913620.29896884X-RAY DIFFRACTION99.92
1.86-1.890.31713610.28346917X-RAY DIFFRACTION99.89
1.89-1.910.33013220.27956891X-RAY DIFFRACTION99.92
1.91-1.940.32713830.26626912X-RAY DIFFRACTION99.92
1.94-1.970.33553880.25666934X-RAY DIFFRACTION99.88
1.97-20.32353530.25126874X-RAY DIFFRACTION99.94
2-2.030.29473450.24436933X-RAY DIFFRACTION99.84
2.03-2.060.273550.23156894X-RAY DIFFRACTION99.93
2.06-2.10.283270.22036960X-RAY DIFFRACTION99.81
2.1-2.130.2633970.21056894X-RAY DIFFRACTION99.88
2.13-2.180.24613650.20186948X-RAY DIFFRACTION99.89
2.18-2.220.25133550.21046881X-RAY DIFFRACTION99.99
2.22-2.270.25893640.19456943X-RAY DIFFRACTION99.89
2.27-2.320.24213410.19056961X-RAY DIFFRACTION99.96
2.32-2.380.25283630.18466957X-RAY DIFFRACTION99.86
2.38-2.440.22573740.17846923X-RAY DIFFRACTION99.82
2.44-2.510.2383660.18676948X-RAY DIFFRACTION99.9
2.51-2.60.23343720.17936969X-RAY DIFFRACTION99.92
2.6-2.690.22233920.17176917X-RAY DIFFRACTION99.96
2.69-2.80.20883950.17526937X-RAY DIFFRACTION99.92
2.8-2.920.24183480.18127008X-RAY DIFFRACTION99.93
2.92-3.080.2473780.1846985X-RAY DIFFRACTION99.96
3.08-3.270.22214270.18856949X-RAY DIFFRACTION99.88
3.27-3.520.20693500.17117052X-RAY DIFFRACTION99.95
3.52-3.880.2033750.15997054X-RAY DIFFRACTION99.95
3.88-4.440.17043710.13697064X-RAY DIFFRACTION99.89
4.44-5.590.16464050.13277130X-RAY DIFFRACTION99.91
5.59-45.050.18334100.16497356X-RAY DIFFRACTION99.21

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