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- PDB-7sx1: human triosephosphate isomerase mutant v154m -

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Basic information

Entry
Database: PDB / ID: 7sx1
Titlehuman triosephosphate isomerase mutant v154m
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / enzyme / glycolysis
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 / canonical glycolysis / glycerol catabolic process / Glycolysis ...methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / glyceraldehyde-3-phosphate biosynthetic process / canonical glycolysis / 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
ISOPROPYL ALCOHOL / Triosephosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsRomero, J.M.
Funding support Argentina, 1items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT) Argentina
CitationJournal: To Be Published
Title: human triosephosphate isomerase mutant v154m
Authors: Romero, J.M.
History
DepositionNov 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)53,5273
Polymers53,4672
Non-polymers601
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-13 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.460, 75.400, 91.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 26733.531 Da / Num. of mol.: 2 / Mutation: V154M
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-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 20% PEG 4000, and 10% 2-propanol
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
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.23→45.78 Å / Num. obs: 22656 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.062 / Rrim(I) all: 0.116 / Net I/σ(I): 8.6 / Num. measured all: 75001 / Scaling rejects: 30
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
2.23-2.32.60.323535120250.8560.2360.4022.898.9
8.92-45.783.40.04214394220.9950.0250.04919.599.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UP1

6up1


Resolution: 2.23→45.78 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.873 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.329 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 1223 5.4 %RANDOM
Rwork0.1675 ---
obs0.1706 21384 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.97 Å2 / Biso mean: 26.15 Å2 / Biso min: 8.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.63 Å2-0 Å20 Å2
2--3.32 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: final / Resolution: 2.23→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 4 284 3996
Biso mean--30.67 30.33 -
Num. residues----491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193788
X-RAY DIFFRACTIONr_bond_other_d0.0020.023593
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9515128
X-RAY DIFFRACTIONr_angle_other_deg0.9438346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2745491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.09725.195154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23315652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.981516
X-RAY DIFFRACTIONr_chiral_restr0.0780.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214251
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02725
LS refinement shellResolution: 2.23→2.288 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 87 -
Rwork0.236 1543 -
all-1630 -
obs--98.19 %

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