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- PDB-1tim: STRUCTURE OF TRIOSE PHOSPHATE ISOMERASE FROM CHICKEN MUSCLE -

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Basic information

Entry
Database: PDB / ID: 1tim
TitleSTRUCTURE OF TRIOSE PHOSPHATE ISOMERASE FROM CHICKEN MUSCLE
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE) / ISOMERASE
Function / homology
Function and homology information


Glycolysis / Glycolysis / Gluconeogenesis / Gluconeogenesis / methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / canonical glycolysis ...Glycolysis / Glycolysis / Gluconeogenesis / Gluconeogenesis / methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / canonical glycolysis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / 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 / Resolution: 2.5 Å
AuthorsBanner, D.W. / Bloomer, A.C. / Petsko, G.A. / Phillips, D.C. / Wilson, I.A.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 1976
Title: Atomic coordinates for triose phosphate isomerase from chicken muscle.
Authors: Banner, D.W. / Bloomer, A. / Petsko, G.A. / Phillips, D.C. / Wilson, I.A.
#1: 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.
#2: Journal: Nature / Year: 1975
Title: Structure of Chicken Muscle Triose Phosphate Isomerase Determined Crystallographically at 2.5 Angstroms 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.
#3: 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.
#4: 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.
#5: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
#6: Journal: Atlas of Protein Sequence and Structure,Supplement 2
Year: 1976
History
DepositionSep 1, 1976Processing site: BNL
Revision 1.0Oct 15, 1976Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)53,1632
Polymers53,1632
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-22 kcal/mol
Surface area20170 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: (0.7199, 0.0924, -0.6879), (0.0953, -0.9949, -0.0339), (-0.6875, -0.0412, -0.725)
Vector: 7.334, 88.423, 30.259)
DetailsTHE MTRIX TRANSFORMATION BELOW WILL TRANSFORM THE COORDINATES OF SUBUNIT 2 (B CHAIN) ONTO THOSE OF SUBUNIT 1 (A CHAIN) WITH AN RMS SEPARATION BETWEEN EQUIVALENT CA ATOMS OF 1.2 ANGSTROMS WHEN THE SUBUNITS ARE SUPERIMPOSED.

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE


Mass: 26581.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P00940, triose-phosphate isomerase
Sequence detailsCHICKEN TRIOSE PHOSPHATE ISOMERASE HAS 247 AMINO ACID RESIDUES BUT HAS THEM NUMBERED 1-2, 4-248. ...CHICKEN TRIOSE PHOSPHATE ISOMERASE HAS 247 AMINO ACID RESIDUES BUT HAS THEM NUMBERED 1-2, 4-248. RESIDUE 3 IS CONSIDERED A GENETIC DELETION ON THE BASIS OF THE 86 PERCENT HOMOLOGY BETWEEN THIS SEQUENCE AND THAT OF RABBIT TRIOSE PHOSPHATE ISOMERASE, WHICH IS ACHIEVED WHEN THIS RESIDUE IS OMITTED.

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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: 46.53 %
Crystal grow
*PLUS
Method: unknown

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Processing

RefinementHighest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3740 0 0 0 3740

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