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- PDB-9fcw: Crystal structure of human Glucose-6-phosphate isomerase with mal... -

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Basic information

Entry
Database: PDB / ID: 9fcw
TitleCrystal structure of human Glucose-6-phosphate isomerase with maleate 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
MALEIC ACID / TRIETHYLENE GLYCOL / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 16, 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
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)253,91911
Polymers252,9204
Non-polymers9997
Water40,2272233
1
A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,0436
Polymers126,4602
Non-polymers5834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14390 Å2
ΔGint-53 kcal/mol
Surface area36250 Å2
MethodPISA
2
C: Glucose-6-phosphate isomerase
D: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,8765
Polymers126,4602
Non-polymers4163
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-56 kcal/mol
Surface area36690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.729, 107.295, 271.228
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
Details: Homodimer / 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, 2240 molecules

#2: 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
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-MAE / MALEIC ACID


Mass: 116.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2233 / 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: 47.29 %
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 Malate 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: ...Details: Protein buffer: 20 mM Tris pH 7.4, 30 mM NaCl, 20 mM Malate 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: 0.976 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: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.4→38.14 Å / Num. obs: 454749 / % possible obs: 98.6 % / Redundancy: 12.9 % / Biso Wilson estimate: 15.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1278 / Rpim(I) all: 0.03666 / Rrim(I) all: 0.1331 / Net I/σ(I): 11.96
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 2.239 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 41170 / CC1/2: 0.478 / Rpim(I) all: 0.7563 / Rrim(I) all: 2.374 / % possible all: 89.35

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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: 1.4→38.14 Å / SU ML: 0.1472 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.6177
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1895 22824 5.03 %
Rwork0.1422 430900 -
obs0.1446 453724 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→38.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17734 0 67 2233 20034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012118328
X-RAY DIFFRACTIONf_angle_d1.186224805
X-RAY DIFFRACTIONf_chiral_restr0.0882682
X-RAY DIFFRACTIONf_plane_restr0.01283207
X-RAY DIFFRACTIONf_dihedral_angle_d6.99722435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.30396570.267212246X-RAY DIFFRACTION84.67
1.42-1.430.30846540.260412924X-RAY DIFFRACTION89.62
1.43-1.450.30747180.25213575X-RAY DIFFRACTION93.77
1.45-1.470.30177520.229714261X-RAY DIFFRACTION98.32
1.47-1.490.2687620.212114285X-RAY DIFFRACTION99.35
1.49-1.510.27547790.199614363X-RAY DIFFRACTION99.34
1.51-1.530.26417330.192214406X-RAY DIFFRACTION99.39
1.53-1.550.23767670.16914409X-RAY DIFFRACTION99.39
1.55-1.580.22857880.163914367X-RAY DIFFRACTION99.44
1.58-1.60.22047740.153214354X-RAY DIFFRACTION99.54
1.6-1.630.21717590.146314410X-RAY DIFFRACTION99.61
1.63-1.660.21657800.138114454X-RAY DIFFRACTION99.7
1.66-1.690.19937290.136114450X-RAY DIFFRACTION99.7
1.69-1.730.27450.131714492X-RAY DIFFRACTION99.63
1.73-1.760.1927990.122714428X-RAY DIFFRACTION99.66
1.76-1.80.20327880.127314429X-RAY DIFFRACTION99.82
1.8-1.850.18977430.120714565X-RAY DIFFRACTION99.83
1.85-1.90.1917830.127714435X-RAY DIFFRACTION99.81
1.9-1.960.20517710.132814481X-RAY DIFFRACTION99.58
1.96-2.020.177980.119914551X-RAY DIFFRACTION99.8
2.02-2.090.17887830.12114460X-RAY DIFFRACTION99.83
2.09-2.170.16577260.115114626X-RAY DIFFRACTION99.82
2.17-2.270.17337970.122714485X-RAY DIFFRACTION99.62
2.27-2.390.16057470.117214633X-RAY DIFFRACTION99.86
2.39-2.540.1646950.118214694X-RAY DIFFRACTION99.82
2.54-2.740.16998600.123414529X-RAY DIFFRACTION99.9
2.74-3.020.17427940.13114678X-RAY DIFFRACTION99.92
3.02-3.450.17387850.137114765X-RAY DIFFRACTION99.94
3.45-4.350.17567730.139514871X-RAY DIFFRACTION99.94
4.35-38.140.18987850.172315274X-RAY DIFFRACTION99.43

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