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- PDB-4pod: Structure of Triosephosphate Isomerase I170V mutant human enzyme. -

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Basic information

Entry
Database: PDB / ID: 4pod
TitleStructure of Triosephosphate Isomerase I170V mutant 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: 1.99 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,7007
Polymers54,4242
Non-polymers2765
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-33 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.659, 70.729, 91.749
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 27211.986 Da / Num. of mol.: 2 / Mutation: I170V
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, 272 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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 1.9 Å3/Da / Density % sol: 35.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 34% 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: 1.99→38.488 Å / Num. all: 132933 / Num. obs: 27738 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.139 / Χ2: 2.119 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.031.70.4749601.326167.4
2.03-2.0720.45510921.218176.9
2.07-2.112.30.49412251.28186.7
2.11-2.152.70.47713151.445192.3
2.15-2.23.40.49613691.441196.7
2.2-2.254.10.51714031.557199.1
2.25-2.314.80.48614111.605199.6
2.31-2.375.50.44514671.461199.7
2.37-2.445.60.41214131.4591100
2.44-2.525.30.37214251.465199.9
2.52-2.615.60.31814251.515199.7
2.61-2.715.30.2914331.741199.9
2.71-2.845.60.24914521.849199.9
2.84-2.995.60.20814372.056199.9
2.99-3.175.70.16514522.247199.9
3.17-3.425.40.13814592.565199.9
3.42-3.7660.11414642.927199.9
3.76-4.315.80.09314683.204199.7
4.31-5.425.80.08214833.097199.4
5.42-405.30.07415853.372199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.02 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.88 Å
Translation2.5 Å45.88 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 4POC

4poc


Resolution: 1.99→38.488 Å / FOM work R set: 0.856 / SU ML: 0.18 / σ(F): 1.36 / Phase error: 21.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 1200 4.33 %RANDOM
Rwork0.1704 ---
obs0.1722 27688 95.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.3 Å2 / Biso mean: 35.24 Å2 / Biso min: 18.3 Å2
Refinement stepCycle: LAST / Resolution: 1.99→38.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3694 0 9 267 3970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043766
X-RAY DIFFRACTIONf_angle_d0.7795102
X-RAY DIFFRACTIONf_chiral_restr0.043578
X-RAY DIFFRACTIONf_plane_restr0.003660
X-RAY DIFFRACTIONf_dihedral_angle_d13.5281361
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9902-2.06980.29941190.272067218668
2.0698-2.1640.25411200.23082729284990
2.164-2.27810.24961200.20663047316799
2.2781-2.42080.22291200.183830463166100
2.4208-2.60770.24931800.180630053185100
2.6077-2.87010.20481200.178931063226100
2.8701-3.28520.19771200.173331013221100
3.2852-4.13820.18841800.148431013281100
4.1382-38.4950.20011200.14673268338899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1590.18750.04560.3989-0.0409-0.0377-0.02930.3794-0.0627-0.19970.06990.106-0.0647-0.21530.00010.33090.033-0.04880.3599-0.02250.2782-9.86211.608-15.321
20.8534-0.2693-0.2150.7802-0.05780.11190.00510.0129-0.0343-0.0281-0.0058-0.0452-0.02950.0082-00.2531-0.01380.0120.2593-0.01070.21863.317.805-7.027
30.95940.37940.03270.209-0.02920.03260.075-0.25210.2593-0.11050.01570.0482-0.10180.18120.00040.2761-0.02480.02660.3097-0.0510.34165.0326.003-0.046
40.13810.2180.01920.3025-0.07510.34-0.00370.07350.1785-0.05570.0035-0.0363-0.05330.07590.00010.214-0.02040.00720.25550.02910.2398-0.48224.919-5.072
50.19230.16770.14070.24450.37620.3173-0.2330.23820.4249-0.07860.09130.09910.0603-0.0288-0.00030.2965-0.0007-0.01970.30670.03710.35791.10530.621-10.791
60.2073-0.12950.0410.18050.04890.02910.09930.15880.149-0.026-0.13120.01330.01350.1188-0.00020.30170.0278-0.04260.34080.03930.3068-11.51623.518-14.763
70.06230.0103-0.2252-0.01170.02040.2248-0.20040.0945-0.29260.09220.0669-0.21710.1978-0.11340.00020.3375-0.01380.05740.29250.00360.36254.13-13.8692.595
80.0645-0.0628-0.01690.07830.06220.0851-0.0820.0672-0.2861-0.3163-0.06240.01970.42760.05-0.00060.42530.00920.01830.3185-0.08110.38086.357-15.65-11.045
90.33860.0310.21730.00530.01580.144-0.09380.275-0.4949-0.2638-0.1956-0.25740.3331-0.2763-0.08780.4031-0.00010.11650.3117-0.10080.50990.334-20.009-0.362
100.29620.0436-0.34690.3151-0.22780.4308-0.066-0.1828-0.1673-0.0987-0.02030.02510.1293-0.2866-0.00010.3051-0.03570.02340.24840.0080.2836-2.58-9.536-4.848
110.11740.1225-0.04870.5433-0.29410.1391-0.0094-0.0847-0.05020.0651-0.01420.0402-0.1-0.0131-00.2514-0.0080.02130.24180.00790.2396-4.658-0.3696.506
120.4660.2668-0.21460.228-0.30240.7138-0.1242-0.2020.5850.0409-0.23040.2099-0.06430.2595-0.010.3101-0.0231-0.00610.3905-0.00380.30375.893-6.06717.36
130.05310.08260.07960.09410.12710.13040.3228-0.49020.16790.4052-0.15870.055-0.2488-0.1673-0.00020.4093-0.00180.04650.47190.07030.3718-0.275-5.85723.166
140.51390.28040.27650.63370.42720.48420.0671-0.1021-0.57250.0627-0.03820.04760.1612-0.15650.23610.2990.01590.03360.30940.14390.3373-5.047-12.32514.434
150.0259-0.01430.0030.04850.06280.07090.1893-0.0575-0.2898-0.0219-0.2173-0.2111-0.36880.2766-00.3258-0.00660.02210.4940.08670.389416.197-10.31913.556
160.07070.06040.06140.08710.09260.1361-0.1078-0.5669-0.18970.2402-0.0495-0.27340.14810.4016-0.00020.3666-0.00110.00160.41720.10840.41973.767-16.98523.832
171.465-0.1861-0.18440.1910.26870.30540.1687-0.6306-0.05850.1724-0.0501-0.09180.21380.1732-0.01820.30230.02020.05030.27670.10460.41562.129-18.4115.195
180.1850.00210.22770.21390.09550.3241-0.1017-0.1498-0.3003-0.1409-0.1473-0.03980.04710.1796-0.04660.36880.06310.08530.30570.06620.45739.517-21.3046.544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:43 )A4 - 43
2X-RAY DIFFRACTION2( CHAIN A AND RESID 44:118 )A44 - 118
3X-RAY DIFFRACTION3( CHAIN A AND RESID 119:152 )A119 - 152
4X-RAY DIFFRACTION4( CHAIN A AND RESID 153:176 )A153 - 176
5X-RAY DIFFRACTION5( CHAIN A AND RESID 177:215 )A177 - 215
6X-RAY DIFFRACTION6( CHAIN A AND RESID 216:247 )A216 - 247
7X-RAY DIFFRACTION7( CHAIN B AND RESID 3:16 )B3 - 16
8X-RAY DIFFRACTION8( CHAIN B AND RESID 17:30 )B17 - 30
9X-RAY DIFFRACTION9( CHAIN B AND RESID 31:43 )B31 - 43
10X-RAY DIFFRACTION10( CHAIN B AND RESID 44:66 )B44 - 66
11X-RAY DIFFRACTION11( CHAIN B AND RESID 67:117 )B67 - 117
12X-RAY DIFFRACTION12( CHAIN B AND RESID 118:137 )B118 - 137
13X-RAY DIFFRACTION13( CHAIN B AND RESID 138:152 )B138 - 152
14X-RAY DIFFRACTION14( CHAIN B AND RESID 153:164 )B153 - 164
15X-RAY DIFFRACTION15( CHAIN B AND RESID 165:176 )B165 - 176
16X-RAY DIFFRACTION16( CHAIN B AND RESID 177:194 )B177 - 194
17X-RAY DIFFRACTION17( CHAIN B AND RESID 195:215 )B195 - 215
18X-RAY DIFFRACTION18( CHAIN B AND RESID 216:246 )B216 - 246

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