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- PDB-6upf: Triosephosphate isomerase deficiency: Effect of F240L mutation on... -

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Basic information

Entry
Database: PDB / ID: 6upf
TitleTriosephosphate isomerase deficiency: Effect of F240L mutation on enzyme structure
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / glycolytic enzyme / alpha beta barrel
Function / homology
Function and homology information


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / Gluconeogenesis / triose-phosphate isomerase / triose-phosphate isomerase activity / canonical glycolysis / Glycolysis ...methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / Gluconeogenesis / triose-phosphate isomerase / triose-phosphate isomerase activity / canonical glycolysis / 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 class I / Aldolase-type TIM barrel / TIM Barrel ...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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRomero, J.M.
CitationJournal: Arch.Biochem.Biophys. / Year: 2020
Title: Triosephosphate isomerase deficiency: Effect of F240L mutation on enzyme structure.
Authors: Romero, J.M.
History
DepositionOct 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 15, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3045
Polymers53,8992
Non-polymers4043
Water12,647702
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-29 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.830, 75.160, 151.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 26949.729 Da / Num. of mol.: 2 / Mutation: F240L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPI1, TPI / Production host: Escherichia coli (E. coli)
References: UniProt: P60174, triose-phosphate isomerase, methylglyoxal synthase
#2: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M Tris-HCl pH 7.5, 0.05 M NaCl, 1 mM EDTA, 15% PEG 4000 and 2 mM 2-PG
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 1.65→75.96 Å / Num. obs: 66128 / % possible obs: 99 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.052 / Rrim(I) all: 0.099 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.65-1.683.40.7141092632080.5230.4420.8451.899.4
9.03-45.623.60.03816924690.9970.0220.04420.695.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4poc

4poc


Resolution: 1.65→75.96 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.065 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.089
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.197 3334 5 %RANDOM
Rwork0.1628 ---
obs0.1646 62725 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 64.3 Å2 / Biso mean: 19.827 Å2 / Biso min: 8.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.14 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.65→75.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3718 0 42 702 4462
Biso mean--21.14 33.34 -
Num. residues----494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193858
X-RAY DIFFRACTIONr_bond_other_d0.0020.023646
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.9615237
X-RAY DIFFRACTIONr_angle_other_deg1.06738485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2525506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.64925.294153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92315657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1131516
X-RAY DIFFRACTIONr_chiral_restr0.1250.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214305
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02723
LS refinement shellResolution: 1.65→1.692 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.301 228 -
Rwork0.295 4571 -
obs--99.21 %

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