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- PDB-7rde: Human Triose Phosphate Isomerase Q181P -

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Basic information

Entry
Database: PDB / ID: 7rde
TitleHuman Triose Phosphate Isomerase Q181P
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TPI / TPI Df
Function / homology
Function and homology information


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / canonical glycolysis / Glycolysis ...methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / 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-type TIM barrel
Similarity search - Domain/homology
BROMIDE ION / Triosephosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsVanDemark, A.P. / Kowalski, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103369 United States
CitationJournal: Dis Model Mech / Year: 2022
Title: Itavastatin and resveratrol increase triosephosphate isomerase protein in a newly identified variant of TPI deficiency.
Authors: VanDemark, A.P. / Hrizo, S.L. / Eicher, S.L. / Kowalski, J. / Myers, T.D. / Pfeifer, M.R. / Riley, K.N. / Koeberl, D.D. / Palladino, M.J.
History
DepositionJul 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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)53,5415
Polymers53,3412
Non-polymers2003
Water9,962553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-28 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.189, 77.822, 84.295
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

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


Mass: 26670.453 Da / Num. of mol.: 2 / Mutation: Q181P
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): BL21(DE3)
References: UniProt: P60174, triose-phosphate isomerase, methylglyoxal synthase
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30% PEG 3350, 50mM Potassium Bromide, Tris pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.308→57.18 Å / Num. obs: 115131 / % possible obs: 98.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 12.47 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.3
Reflection shellResolution: 1.308→1.331 Å / Redundancy: 6.3 % / Num. unique obs: 5679 / CC1/2: 0.701 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NLH

6nlh


Resolution: 1.31→35.33 Å / SU ML: 0.1165 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.9839 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.162 1982 1.72 %
Rwork0.1368 113109 -
obs0.1373 115091 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.77 Å2
Refinement stepCycle: LAST / Resolution: 1.31→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3614 0 3 553 4170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093682
X-RAY DIFFRACTIONf_angle_d1.03174985
X-RAY DIFFRACTIONf_chiral_restr0.0823562
X-RAY DIFFRACTIONf_plane_restr0.0073645
X-RAY DIFFRACTIONf_dihedral_angle_d15.17591335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.340.24441380.22717932X-RAY DIFFRACTION98.19
1.34-1.380.22651420.20688011X-RAY DIFFRACTION98.91
1.38-1.420.19171300.1758022X-RAY DIFFRACTION98.85
1.42-1.460.18281520.14888012X-RAY DIFFRACTION98.93
1.46-1.520.17871260.12667982X-RAY DIFFRACTION98.79
1.52-1.580.15821530.12057935X-RAY DIFFRACTION97.98
1.58-1.650.15061290.11358056X-RAY DIFFRACTION99.06
1.65-1.740.15331560.1148069X-RAY DIFFRACTION99.17
1.74-1.840.13971380.11818120X-RAY DIFFRACTION99.3
1.84-1.990.13881360.12188015X-RAY DIFFRACTION98.37
1.99-2.190.14811480.12478153X-RAY DIFFRACTION99.43
2.19-2.50.14641410.12468187X-RAY DIFFRACTION99.47
2.5-3.150.16981430.14188162X-RAY DIFFRACTION98.27
3.15-35.330.16671500.1478453X-RAY DIFFRACTION98.56

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