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- PDB-9f69: Crystal structure of human triose phosphate isomerase with methyl... -

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Basic information

Entry
Database: PDB / ID: 9f69
TitleCrystal structure of human triose phosphate isomerase with methyl malonic acid 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 / triose-phosphate isomerase activity / Gluconeogenesis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / canonical glycolysis / Glycolysis ...methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / canonical glycolysis / Glycolysis / glycolytic process / gluconeogenesis / 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 / METHYLMALONIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 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
DepositionApr 30, 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: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5133
Polymers26,3151
Non-polymers1982
Water5,441302
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0266
Polymers52,6302
Non-polymers3964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area3520 Å2
ΔGint-16 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.466, 48.466, 341.862
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-404-

HOH

21A-597-

HOH

31A-641-

HOH

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Components

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


Mass: 26314.998 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) / Strain (production host): Lemo 21
References: UniProt: P60174, triose-phosphate isomerase, methylglyoxal synthase
#2: Chemical ChemComp-DXX / METHYLMALONIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / 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.: 302 / 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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
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 24 mM methylmalonate (pH adjusted to 7.4), mother liquor, and cryo-protectant Ligand soaking and cryoprotectant were performed simultaneously
Temp details: Room temp

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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: 1.17→31.83 Å / Num. obs: 82312 / % possible obs: 99.81 % / Redundancy: 34.8 % / Biso Wilson estimate: 13.39 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1163 / Rpim(I) all: 0.01965 / Net I/σ(I): 23.55
Reflection shellResolution: 1.17→1.212 Å / Redundancy: 20.4 % / Mean I/σ(I) obs: 1.23 / Num. unique obs: 8037 / CC1/2: 0.437 / CC star: 0.78 / Rpim(I) all: 0.6615 / % possible all: 99.06

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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: 1.17→31.83 Å / SU ML: 0.1152 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.886
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1837 4096 4.98 %
Rwork0.1465 78135 -
obs0.1484 82231 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.94 Å2
Refinement stepCycle: LAST / Resolution: 1.17→31.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 9 302 2161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871899
X-RAY DIFFRACTIONf_angle_d1.0472574
X-RAY DIFFRACTIONf_chiral_restr0.0756291
X-RAY DIFFRACTIONf_plane_restr0.0106335
X-RAY DIFFRACTIONf_dihedral_angle_d6.7625261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.17-1.180.30711490.28352600X-RAY DIFFRACTION98.14
1.18-1.20.30771440.27612595X-RAY DIFFRACTION99.49
1.2-1.210.27481420.26042668X-RAY DIFFRACTION99.47
1.21-1.230.26861450.24162546X-RAY DIFFRACTION99.67
1.23-1.250.31481370.2262658X-RAY DIFFRACTION99.79
1.25-1.260.22571400.21182591X-RAY DIFFRACTION99.85
1.26-1.280.25871220.21262693X-RAY DIFFRACTION99.82
1.28-1.30.24911370.20262621X-RAY DIFFRACTION99.93
1.3-1.320.27521390.20032638X-RAY DIFFRACTION100
1.32-1.350.25571440.19792690X-RAY DIFFRACTION99.93
1.35-1.370.24521460.18442599X-RAY DIFFRACTION99.85
1.37-1.40.28191360.17442668X-RAY DIFFRACTION99.96
1.4-1.430.21181630.16252671X-RAY DIFFRACTION100
1.43-1.460.20251290.14092634X-RAY DIFFRACTION99.82
1.46-1.490.19421370.1392655X-RAY DIFFRACTION100
1.49-1.530.17371460.13742676X-RAY DIFFRACTION99.96
1.53-1.570.20461680.132636X-RAY DIFFRACTION99.89
1.57-1.620.18971240.12292735X-RAY DIFFRACTION99.97
1.62-1.670.1461490.11122653X-RAY DIFFRACTION99.96
1.67-1.730.17631200.11552705X-RAY DIFFRACTION99.96
1.73-1.80.19551430.11662700X-RAY DIFFRACTION99.93
1.8-1.880.16021320.1192716X-RAY DIFFRACTION99.89
1.88-1.980.15921280.12022708X-RAY DIFFRACTION99.86
1.98-2.10.14291190.11742795X-RAY DIFFRACTION99.86
2.1-2.260.14441410.1192719X-RAY DIFFRACTION99.93
2.26-2.490.14921420.13342778X-RAY DIFFRACTION99.93
2.49-2.850.17981320.13772848X-RAY DIFFRACTION99.97
2.85-3.590.16021660.13592832X-RAY DIFFRACTION100
3.59-31.830.1891760.16093107X-RAY DIFFRACTION99.88

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