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- PDB-1ypi: STRUCTURE OF YEAST TRIOSEPHOSPHATE ISOMERASE AT 1.9-ANGSTROMS RES... -

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Basic information

Entry
Database: PDB / ID: 1ypi
TitleSTRUCTURE OF YEAST TRIOSEPHOSPHATE ISOMERASE AT 1.9-ANGSTROMS RESOLUTION
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
Function / homology
Function and homology information


Gluconeogenesis / Glycolysis / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / mitochondrion / plasma membrane ...Gluconeogenesis / Glycolysis / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / mitochondrion / plasma membrane / cytoplasm / 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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsAlber, T. / Lolis, E. / Petsko, G.A.
Citation
Journal: Biochemistry / Year: 1990
Title: Structure of yeast triosephosphate isomerase at 1.9-A resolution.
Authors: Lolis, E. / Alber, T. / Davenport, R.C. / Rose, D. / Hartman, F.C. / Petsko, G.A.
#1: Journal: Biochemistry / Year: 1990
Title: Crystallographic Analysis of the Complex between Triosephosphate Isomerase and 2-Phosphoglycolate at 2.5-Angstroms Resolution. Implications for Catalysis
Authors: Lolis, E. / Petsko, G.A.
#2: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1987
Title: Crystallography and Site-Directed Mutagenesis of Yeast Triosephosphate Isomerase. What Can We Learn About Catalysis from a (Double Quote)Simple(Double Quote) Enzyme (Question Mark)
Authors: Alber, T.C. / Davenportjunior, R.C. / Giammona, D.A. / Lolis, E. / Petsko, G.A. / Ringe, D.
#3: Journal: J.Biol.Chem. / Year: 1981
Title: Crystallization of Yeast Triose Phosphate Isomerase from Polyethylene Glycol. Protein Crystal Formation Following Phase Separation
Authors: Alber, T. / Hartman, F.C. / Johnson, R.M. / Petsko, G.A. / Tsernoglou, D.
#4: 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.
History
DepositionJan 12, 1990Processing site: BNL
Revision 1.0Jan 15, 1991Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Remark 700SHEET THE SHEETS PRESENTED AS *BLA* AND *BLB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED ...SHEET THE SHEETS PRESENTED AS *BLA* AND *BLB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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


Theoretical massNumber of molelcules
Total (without water)53,3922
Polymers53,3922
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-10 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.150, 98.550, 49.260
Angle α, β, γ (deg.)90.00, 91.20, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES LYS A 12, ASN A 28, ASN A 35, HIS A 103, ARG B 3, HIS B 103, LEU B 131, ASP B 222 HAVE DIHEDRAL ANGLES THAT ARE SIGNIFICANTLY OUTSIDE THE RAMACHANDRAN LIMITS.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1.00004, -0.00217, -0.00079), (-0.0017, 0.43502, 0.90043), (-0.00226, 0.90281, -0.43581)
Vector: 120.42589, -12.98956, 20.80916)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE


Mass: 26696.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00942, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE NUMBERING IN EACH CHAIN IS SEQUENTIAL STARTING WITH 2.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion / Details: can also be done with bathch methods
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlyeast triosephosphate isomerase1reservoir
212 %satammonium sulfate1reservoir
31 mMEDTA1reservoir
41 mMmercaptoethanol1reservoir
550 mMTris-HCl1reservoir
616 %PEG40001reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 3 Å / Num. obs: 2028 / Rmerge(I) obs: 0.113

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→40 Å
Details: RESIDUES LYS A 12, ASN A 28, ASN A 35, HIS A 103, ARG B 3, HIS B 103, LEU B 131, ASP B 222 HAVE DIHEDRAL ANGLES THAT ARE SIGNIFICANTLY OUTSIDE THE RAMACHANDRAN LIMITS.
RfactorNum. reflection
obs0.21 35167
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 0 119 3885
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0250.03
X-RAY DIFFRACTIONp_angle_d0.0480.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0550.052
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
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 40 Å / Num. reflection obs: 35167 / Rfactor obs: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2.06 Å / Total num. of bins used: 7 / Num. reflection obs: 4880 / Rfactor obs: 0.253

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