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- PDB-9fkf: Crystal structure of human Glucose-6-phosphate isomerase with pho... -

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Basic information

Entry
Database: PDB / ID: 9fkf
TitleCrystal structure of human Glucose-6-phosphate isomerase with phosphoenol pyruvate 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 / monosaccharide binding / fructose 6-phosphate metabolic process / Glycolysis / erythrocyte homeostasis ...glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / monosaccharide binding / fructose 6-phosphate metabolic process / Glycolysis / erythrocyte homeostasis / ciliary membrane / positive regulation of immunoglobulin production / response to testosterone / humoral immune response / mesoderm formation / response to immobilization stress / response to cadmium ion / response to muscle stretch / positive regulation of endothelial cell migration / response to progesterone / cytokine activity / gluconeogenesis / glycolytic process / TP53 Regulates Metabolic Genes / growth factor activity / glucose homeostasis / response to estradiol / secretory granule lumen / in utero embryonic development / carbohydrate metabolic process / ficolin-1-rich granule lumen / 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
DI(HYDROXYETHYL)ETHER / PHOSPHOENOLPYRUVATE / 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

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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)254,37714
Polymers252,9204
Non-polymers1,45710
Water20,5551141
1
A: Glucose-6-phosphate isomerase
C: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,3258
Polymers126,4602
Non-polymers8656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15280 Å2
ΔGint-54 kcal/mol
Surface area36330 Å2
MethodPISA
2
B: Glucose-6-phosphate isomerase
D: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,0526
Polymers126,4602
Non-polymers5924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13460 Å2
ΔGint-70 kcal/mol
Surface area36670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.840, 107.482, 271.193
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 , 5 types, 1151 molecules

#2: Chemical
ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1141 / 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: 2.33 Å3/Da / Density % sol: 47.19 %
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 PEP 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 ...Details: Protein buffer: 20 mM Tris pH 7.4, 30 mM NaCl, 20 mM PEP 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: 1.6→48.42 Å / Num. obs: 310109 / % possible obs: 99.76 % / Redundancy: 13.5 % / Biso Wilson estimate: 19.17 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1929 / Rpim(I) all: 0.05442 / Rrim(I) all: 0.2006 / Net I/σ(I): 9.89
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 13.6 % / Rmerge(I) obs: 3.025 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 30723 / CC1/2: 0.671 / CC star: 0.896 / Rpim(I) all: 0.8441 / Rrim(I) all: 3.142 / % possible all: 99.79

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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→48.42 Å / SU ML: 0.194 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.4266
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2235 15554 5.02 %
Rwork0.1869 294015 -
obs0.1887 309569 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.32 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17727 0 92 1141 18960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015418251
X-RAY DIFFRACTIONf_angle_d1.357924696
X-RAY DIFFRACTIONf_chiral_restr0.07672671
X-RAY DIFFRACTIONf_plane_restr0.01483184
X-RAY DIFFRACTIONf_dihedral_angle_d7.64312416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.32285250.29829776X-RAY DIFFRACTION99.82
1.62-1.640.31715430.29219612X-RAY DIFFRACTION99.75
1.64-1.660.32955140.28429704X-RAY DIFFRACTION99.79
1.66-1.680.33554960.28149768X-RAY DIFFRACTION99.7
1.68-1.70.30925100.26859680X-RAY DIFFRACTION99.77
1.7-1.720.31185500.26259674X-RAY DIFFRACTION99.64
1.72-1.750.26935130.24829689X-RAY DIFFRACTION99.56
1.75-1.770.30045050.24739717X-RAY DIFFRACTION99.66
1.77-1.80.26655040.239780X-RAY DIFFRACTION99.71
1.8-1.830.28385050.22389700X-RAY DIFFRACTION99.71
1.83-1.860.275360.21959694X-RAY DIFFRACTION99.69
1.86-1.90.27575400.21289714X-RAY DIFFRACTION99.78
1.9-1.930.24925060.20299748X-RAY DIFFRACTION99.77
1.93-1.970.26295120.20179794X-RAY DIFFRACTION99.81
1.97-2.020.25145330.20499715X-RAY DIFFRACTION99.81
2.02-2.060.23355000.19789799X-RAY DIFFRACTION99.84
2.06-2.110.22775180.19229735X-RAY DIFFRACTION99.66
2.11-2.170.2265260.18289749X-RAY DIFFRACTION99.58
2.17-2.240.21515260.18299763X-RAY DIFFRACTION99.71
2.24-2.310.23625230.17819784X-RAY DIFFRACTION99.76
2.31-2.390.20065140.16919813X-RAY DIFFRACTION99.83
2.39-2.490.21255330.16989784X-RAY DIFFRACTION99.86
2.49-2.60.22665280.17429840X-RAY DIFFRACTION99.93
2.6-2.740.22114810.17649871X-RAY DIFFRACTION99.95
2.74-2.910.21835150.17839886X-RAY DIFFRACTION99.88
2.91-3.130.21525320.17779876X-RAY DIFFRACTION99.89
3.13-3.450.19944990.17819934X-RAY DIFFRACTION99.91
3.45-3.950.19475130.164510000X-RAY DIFFRACTION99.95
3.95-4.970.17675360.149910041X-RAY DIFFRACTION99.89
4.97-48.420.19735180.180910375X-RAY DIFFRACTION99.44

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