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- PDB-4poc: Structure of Triosephosphate Isomerase Wild Type human enzyme. -

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Basic information

Entry
Database: PDB / ID: 4poc
TitleStructure of Triosephosphate Isomerase Wild Type human enzyme.
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM Alpha/Beta Barrel / TIM Barrel / Glycolytic
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 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
BROMIDE ION / : / PHOSPHATE ION / Triosephosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.601 Å
AuthorsAmrich, C.G. / Aslam, A.A. / Heroux, A. / VanDemark, A.P.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: Triosephosphate isomerase I170V alters catalytic site, enhances stability and induces pathology in a Drosophila model of TPI deficiency.
Authors: Roland, B.P. / Amrich, C.G. / Kammerer, C.J. / Stuchul, K.A. / Larsen, S.B. / Rode, S. / Aslam, A.A. / Heroux, A. / Wetzel, R. / VanDemark, A.P. / Palladino, M.J.
History
DepositionFeb 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,8088
Polymers54,4522
Non-polymers3566
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-38 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.920, 48.851, 93.966
Angle α, β, γ (deg.)90.000, 103.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 27226.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPI, TPI1 / Plasmid: pLC3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+RILP / References: UniProt: P60174, triose-phosphate isomerase

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Non-polymers , 5 types, 333 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 1.96 Å3/Da / Density % sol: 37.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 35% PEG 2000 MME, 0.05 KBr, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2012
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 55891 / Num. obs: 52380 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 25.84 Å2 / Rmerge(I) obs: 0.077 / Χ2: 2.204 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.6330.44215250.684154.2
1.63-1.663.20.43817090.688162.6
1.66-1.693.60.39620850.719175.3
1.69-1.7240.36924420.713188
1.72-1.764.70.34527610.814199.5
1.76-1.85.20.29527640.8981100
1.8-1.856.10.26727860.9981100
1.85-1.96.40.22427861.1331100
1.9-1.956.20.19627961.3391100
1.95-2.026.30.16627651.5771100
2.02-2.096.30.1527811.819199.9
2.09-2.176.40.12827712.0511100
2.17-2.276.40.10927912.2811100
2.27-2.396.10.09927852.5571100
2.39-2.546.20.08627912.53199.9
2.54-2.746.40.07527852.706199.9
2.74-3.016.10.06728093.058199.6
3.01-3.456.10.06227883.541199.3
3.45-4.345.80.06727924.635198.6
4.34-505.10.07128685.518198.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.94 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.56 Å
Translation2.5 Å46.56 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JK2

2jk2


Resolution: 1.601→46.564 Å / FOM work R set: 0.8641 / SU ML: 0.19 / σ(F): 0 / Phase error: 20.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 2695 5.15 %RANDOM
Rwork0.153 ---
all0.225 55891 --
obs0.1548 52340 93.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.29 Å2 / Biso mean: 36.13 Å2 / Biso min: 19.19 Å2
Refinement stepCycle: LAST / Resolution: 1.601→46.564 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3719 0 10 327 4056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053792
X-RAY DIFFRACTIONf_angle_d0.9625137
X-RAY DIFFRACTIONf_chiral_restr0.052581
X-RAY DIFFRACTIONf_plane_restr0.004665
X-RAY DIFFRACTIONf_dihedral_angle_d15.1111374
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6011-1.63020.3406680.24251489155753
1.6302-1.66150.27661040.22371747185164
1.6615-1.69550.22251340.1962097223176
1.6955-1.73230.23051440.18082479262391
1.7323-1.77260.20261560.173727662922100
1.7726-1.8170.23311370.170627822919100
1.817-1.86610.23061420.159227882930100
1.8661-1.9210.20581460.15327972943100
1.921-1.9830.21261370.15627662903100
1.983-2.05390.18421650.159427732938100
2.0539-2.13610.21521670.160927662933100
2.1361-2.23330.17891640.143827632927100
2.2333-2.35110.17651210.143328262947100
2.3511-2.49840.20881450.150127842929100
2.4984-2.69130.20251630.15327712934100
2.6913-2.9620.18521500.152428162966100
2.962-3.39060.1961540.15232783293799
3.3906-4.27130.15631450.13932793293899
4.2713-46.5840.17161530.15582859301299

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