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- PDB-6d43: CHARACTERIZATION OF HUMAN TRIOSEPHOSPHATE ISOMERASE S-NITROSYLATION -

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Basic information

Entry
Database: PDB / ID: 6d43
TitleCHARACTERIZATION OF HUMAN TRIOSEPHOSPHATE ISOMERASE S-NITROSYLATION
Components(Triosephosphate isomerase) x 2
KeywordsISOMERASE / S-nitrosylation / glycolysis / TIM-barrel / Dihydroxyacetone phosphate
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 / 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
ISOPROPYL ALCOHOL / Triosephosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.04 Å
AuthorsRomero, J.M. / Carrizo, M.E. / Curtino, J.M.
Funding support Argentina, 1items
OrganizationGrant numberCountry
National Research Council (NRC, Argentina)PIP 11220120100637CO Argentina
CitationJournal: Nitric Oxide / Year: 2018
Title: Characterization of human triosephosphate isomerase S-nitrosylation.
Authors: Romero, J.M. / Carrizo, M.E. / Curtino, J.A.
History
DepositionApr 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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)52,8933
Polymers52,8332
Non-polymers601
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-12 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.920, 73.980, 93.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 26431.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: S-nitrosylation at residue 217 / Source: (gene. exp.) Homo sapiens (human) / Gene: TPI1, TPI / Production host: Escherichia coli (E. coli) / References: UniProt: P60174, triose-phosphate isomerase
#2: Protein Triosephosphate isomerase / TIM / Triose-phosphate isomerase


Mass: 26402.076 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 (E. coli) / References: UniProt: P60174, triose-phosphate isomerase
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


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


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 20% PEG 4000, and 10% 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.04→58.09 Å / Num. obs: 27988 / % possible obs: 95.2 % / Redundancy: 4.7 % / CC1/2: 0.919 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.068 / Rrim(I) all: 0.145 / Net I/σ(I): 8.2
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.301 / Num. unique obs: 1904 / CC1/2: 0.567 / Rpim(I) all: 0.163 / Rrim(I) all: 0.346 / % possible all: 89.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimless0.5.17data scaling
PDB_EXTRACT3.24data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2JK2

2jk2


Resolution: 2.04→58.09 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.844 / SU B: 7.893 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 1327 4.7 %RANDOM
Rwork0.2018 ---
obs0.20444 26617 94.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.081 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å2-0 Å2
2--1.62 Å2-0 Å2
3----1.48 Å2
Refinement stepCycle: 1 / Resolution: 2.04→58.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 4 366 4078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193786
X-RAY DIFFRACTIONr_bond_other_d0.0020.023680
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.9525128
X-RAY DIFFRACTIONr_angle_other_deg0.90238479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9495491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.7725.195154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12515644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.9211516
X-RAY DIFFRACTIONr_chiral_restr0.0680.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024327
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02817
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7561.7551967
X-RAY DIFFRACTIONr_mcbond_other0.7561.7551966
X-RAY DIFFRACTIONr_mcangle_it1.3052.6292457
X-RAY DIFFRACTIONr_mcangle_other1.3052.632458
X-RAY DIFFRACTIONr_scbond_it0.7271.8181819
X-RAY DIFFRACTIONr_scbond_other0.7261.8181820
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2642.6942672
X-RAY DIFFRACTIONr_long_range_B_refined3.24614.2334539
X-RAY DIFFRACTIONr_long_range_B_other2.94914.0374412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.037→2.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 106 -
Rwork0.186 1791 -
obs--88.56 %

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