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- PDB-9ffc: Crystal structure of human triose phosphate isomerase with glycer... -

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Basic information

Entry
Database: PDB / ID: 9ffc
TitleCrystal structure of human triose phosphate isomerase with glycerol-3-phosphate ligand
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / Metabolic regulation / glycolysis / modular inhibition
Function / homology
Function and homology information


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / Gluconeogenesis / triose-phosphate isomerase activity / canonical glycolysis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / Glycolysis ...methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / Gluconeogenesis / triose-phosphate isomerase activity / canonical glycolysis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / Glycolysis / gluconeogenesis / glycolytic process / ubiquitin protein ligase binding / protein homodimerization activity / extracellular space / extracellular exosome / nucleus / cytosol
Similarity search - Function
Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
BROMIDE ION / SN-GLYCEROL-3-PHOSPHATE / Triosephosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 23, 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

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Assembly

Deposited unit
A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9533
Polymers26,7011
Non-polymers2522
Water4,792266
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9076
Polymers53,4032
Non-polymers5044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4180 Å2
ΔGint-28 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.860, 48.860, 342.156
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-443-

HOH

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Components

#1: Protein Triosephosphate isomerase / TIM / Methylglyoxal synthase / Triose-phosphate isomerase


Mass: 26701.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPI1, TPI / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21
References: UniProt: P60174, triose-phosphate isomerase, methylglyoxal synthase
#2: Chemical ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Protein buffer: 20 mM Tris pH 7.4, 30 mM NaCl. Reservoir: 0.14 M KBr, 24% PEG 2000 MME. Hanging drop: 1.5:1.5:1.0 ul - Reservoir-Protein (8 mg/ml)-Seed stock. Cryoprotectant = 20% glycerol; ...Details: Protein buffer: 20 mM Tris pH 7.4, 30 mM NaCl. Reservoir: 0.14 M KBr, 24% PEG 2000 MME. Hanging drop: 1.5:1.5:1.0 ul - Reservoir-Protein (8 mg/ml)-Seed stock. Cryoprotectant = 20% glycerol; Ligand soaking performed for 5-6 min in a mixture containing 20 mM glycerol-3-phosphate (pH adjusted to 7.4), mother liquor, and cryo-protectant Ligand soaking and cryoprotectant were performed simultaneously

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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: Feb 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.25→25.06 Å / Num. obs: 68952 / % possible obs: 99.59 % / Redundancy: 36.4 % / Biso Wilson estimate: 14.55 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06885 / Rpim(I) all: 0.01171 / Rrim(I) all: 0.06988 / Net I/σ(I): 28.46
Reflection shellResolution: 1.25→1.295 Å / Rmerge(I) obs: 0.9524 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 6688 / CC1/2: 0.99 / CC star: 0.997 / Rpim(I) all: 0.1565 / Rrim(I) all: 0.9654 / % possible all: 99.46

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→25.06 Å / SU ML: 0.1115 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.2137
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1801 3503 5.1 %
Rwork0.146 65212 -
obs0.1478 68715 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.98 Å2
Refinement stepCycle: LAST / Resolution: 1.25→25.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 0 11 266 2133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861899
X-RAY DIFFRACTIONf_angle_d1.04892572
X-RAY DIFFRACTIONf_chiral_restr0.08290
X-RAY DIFFRACTIONf_plane_restr0.0106332
X-RAY DIFFRACTIONf_dihedral_angle_d6.6894262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.22291320.18842499X-RAY DIFFRACTION99.47
1.27-1.290.28511300.19252599X-RAY DIFFRACTION99.53
1.29-1.30.25581050.1782521X-RAY DIFFRACTION99.47
1.3-1.320.22811260.16852578X-RAY DIFFRACTION99.45
1.32-1.350.21291300.16842534X-RAY DIFFRACTION99.4
1.35-1.370.22281550.15772521X-RAY DIFFRACTION99.26
1.37-1.390.18451250.15052575X-RAY DIFFRACTION99.37
1.39-1.420.1881300.152506X-RAY DIFFRACTION98.91
1.42-1.450.21921410.14422557X-RAY DIFFRACTION99.05
1.45-1.480.19021360.14492588X-RAY DIFFRACTION99.2
1.48-1.520.18981390.14542537X-RAY DIFFRACTION99.7
1.52-1.550.21521410.14542562X-RAY DIFFRACTION99.59
1.55-1.60.21461460.13732584X-RAY DIFFRACTION99.6
1.6-1.640.20291320.13162581X-RAY DIFFRACTION99.89
1.64-1.70.18611340.12922601X-RAY DIFFRACTION99.6
1.7-1.760.16851360.13042581X-RAY DIFFRACTION99.41
1.76-1.830.17391500.12592585X-RAY DIFFRACTION99.82
1.83-1.910.15551440.1352621X-RAY DIFFRACTION99.93
1.91-2.010.15841670.1282609X-RAY DIFFRACTION99.96
2.01-2.140.17621380.13342642X-RAY DIFFRACTION99.86
2.14-2.30.14191360.1322661X-RAY DIFFRACTION99.96
2.3-2.530.18391540.13922683X-RAY DIFFRACTION99.96
2.53-2.90.17481510.1412709X-RAY DIFFRACTION100
2.9-3.650.15591620.14642753X-RAY DIFFRACTION100
3.65-25.060.20021630.16673025X-RAY DIFFRACTION99.87

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