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- PDB-8tim: TRIOSE PHOSPHATE ISOMERASE -

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Basic information

Entry
Database: PDB / ID: 8tim
TitleTRIOSE PHOSPHATE ISOMERASE
ComponentsTRIOSE PHOSPHATE ISOMERASETriosephosphate isomerase
KeywordsISOMERASE / GLYCOLYSIS / GLUCONEOGENESIS / FATTY ACID BIOSYNTHESIS
Function / homology
Function and homology information


Glycolysis / Glycolysis / Gluconeogenesis / Gluconeogenesis / methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase ...Glycolysis / Glycolysis / Gluconeogenesis / Gluconeogenesis / methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / canonical glycolysis / gluconeogenesis / glycolytic process / ubiquitin protein ligase binding / protein homodimerization activity / 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
Triosephosphate isomerase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsArtymiuk, P.J. / Taylor, W.R. / Phillips, D.C.
Citation
Journal: To be Published
Title: Triose Phosphate Isomerase
Authors: Artymiuk, P.J. / Taylor, W.R. / Phillips, D.C.
#1: Journal: Am.J.Hum.Genet. / Year: 1993
Title: Human Triosephosphate Isomerase Deficiency Resulting from Mutation of Phe-240
Authors: Chang, M.L. / Artymiuk, P.J. / Wu, X. / Hollan, S. / Lammi, A. / Maquat, L.E.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1986
Title: Human Triose-Phosphate Isomerase Deficiency: A Single Amino Acid Substitution Results in a Thermolabile Enzyme
Authors: Daar, I.O. / Artymiuk, P.J. / Phillips, D.C. / Maquat, L.E.
#3: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1981
Title: On the Three-Dimensional Structure and Catalytic Mechanism of Triose Phosphate Isomerase
Authors: Alber, T. / Banner, D.W. / Bloomer, A.C. / Petsko, G.A. / Phillips, D. / Rivers, P.S. / Wilson, I.A.
#4: Journal: Biochem.Biophys.Res.Commun. / Year: 1976
Title: Atomic Coordinates for Triose Phosphate Isomerase from Chicken Muscle
Authors: Banner, D.W. / Bloomer, A.C. / Petsko, G.A. / Phillips, D.C. / Wilson, I.A.
#5: Journal: J.Mol.Biol. / Year: 1976
Title: Studies of the Histidine Residues of Triose Phosphate Isomerase by Proton Magnetic Resonance and X-Ray Crystallography
Authors: Browne, C.A. / Campbell, I.D. / Kiener, P.A. / Phillips, D.C. / Waley, S.G. / Wilson, I.A.
#8: Journal: Nature / Year: 1975
Title: Structure of Chicken Muscle Triose Phosphate Isomerase Determined Crystallographically at 2.5 Angstrom Resolution Using Amino Acid Sequence Data
Authors: Banner, D.W. / Bloomer, A.C. / Petsko, G.A. / Phillips, D.C. / Pogson, C.I. / Wilson, I.A. / Corran, P.H. / Furth, A.J. / Milman, J.D. / Offord, R.E. / Priddle, J.D. / Waley, S.G.
#9: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: Crystallographic Studies of Chicken Triose Phosphate Isomerase
Authors: Banner, D.W. / Bloomer, A.C. / Petsko, G.A. / Phillips, D.C. / Pogson, C.I.
#6: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
#7: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1976
History
DepositionAug 25, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: TRIOSE PHOSPHATE ISOMERASE
B: TRIOSE PHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2734
Polymers53,0812
Non-polymers1922
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-47 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.010, 74.760, 61.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.72691, 0.09842, -0.67964), (0.10101, -0.99424, -0.03594), (-0.67926, -0.04253, -0.73266)
Vector: 6.66288, 88.10081, 29.74523)

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Components

#1: Protein TRIOSE PHOSPHATE ISOMERASE / Triosephosphate isomerase


Mass: 26540.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cell line: 293 / Organ: BREAST / Tissue: MUSCLESkeletal muscle / References: UniProt: P00940, triose-phosphate isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHICKEN TRIOSE PHOSPHATE ISOMERASE HAS 247 AMINO ACID RESIDUES. THEY ARE NUMBERED 2-248 FOR EASE OF ...CHICKEN TRIOSE PHOSPHATE ISOMERASE HAS 247 AMINO ACID RESIDUES. THEY ARE NUMBERED 2-248 FOR EASE OF COMPARISON WITH THE SEQUENCE OF RABBIT TRIOSE PHOSPHATE ISOMERASE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceType: OTHER / Wavelength: 1.5418
DetectorType: HILGER-WATTS / Detector: DIFFRACTOMETER / Date: Apr 1, 1975
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. obs: 17023

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementMethod to determine structure: MIR / Resolution: 2.5→10 Å / σ(F): 0
RfactorNum. reflection% reflection
all0.177 --
obs-17023 100 %
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3734 0 10 34 3778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.029
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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