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- PDB-1tpb: OFFSET OF A CATALYTIC LESION BY A BOUND WATER SOLUBLE -

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Basic information

Entry
Database: PDB / ID: 1tpb
TitleOFFSET OF A CATALYTIC LESION BY A BOUND WATER SOLUBLE
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
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
PHOSPHOGLYCOLOHYDROXAMIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsZhang, Z. / Sugio, S. / Komives, E.A. / Liu, K.D. / Knowles, J.R. / Petsko, G.A. / Ringe, D.
Citation
Journal: Biochemistry / Year: 1995
Title: The structural basis for pseudoreversion of the E165D lesion by the secondary S96P mutation in triosephosphate isomerase depends on the positions of active site water molecules.
Authors: Komives, E.A. / Lougheed, J.C. / Liu, K. / Sugio, S. / Zhang, Z. / Petsko, G.A. / Ringe, D.
#1: Journal: To be Published
Title: Offset of a Catalytic Lesion (Glu165Asp) of Triosephosphate Isomerase by Bound Waters Soluble
Authors: Zhang, Z. / Komives, E.A. / Sugio, S. / Liu, K.D. / Knowles, J.R. / Petsko, G.A. / Ringe, D.
#2: Journal: To be Published
Title: Triosephosphate Isomerase Drinks Water to Keep Healthy
Authors: Zhang, Z. / Sugio, S. / Stock, A.M. / Komives, E.A. / Liu, K.D. / Narayana, N. / Huong, Ng.H. / Knowles, J.R. / Petsko, G.A. / Ringe, D.
#3: Journal: To be Published
Title: The Structural Basis for Pseudoreversion of the E165D Lesion by the Secondary S96P Mutation in Triosephosphate Isomerase Depends on the Position of Bound Water Molecules
Authors: Komives, E.A. / Lougheed, J.C. / Zhang, Z. / Petsko, G.A. / Ringe, D.
#4: Journal: To be Published
Title: S96P Change is the Second-Site Suppressor for the H95N Sluggish Mutant Isomerase
Authors: Zhang, Z. / Sugio, S. / Komives, E.A. / Liu, K.D. / Stock, A.M. / Narayana, N. / Xuong, Ng.H. / Knowles, J.R. / Petsko, G.A. / Ringe, D.
#5: Journal: Biochemistry / Year: 1990
Title: How Can a Catalytic Lesion be Offset? the Energetics of Two Pseudorevertant Triosephosphate Isomerases
Authors: Blacklow, S.C. / Knowles, J.R.
History
DepositionFeb 3, 1994Processing site: BNL
Revision 1.0Feb 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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
1: TRIOSEPHOSPHATE ISOMERASE
2: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3954
Polymers53,0532
Non-polymers3422
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-33 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.400, 74.100, 57.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE


Mass: 26526.264 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
#2: Chemical ChemComp-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.5 MPGH1drop0.0048ml
3100 mMTris-HCl1reservoir
4200 mMlithium sulfate1reservoir
512.5-21 %PEG80001reservoirin 2.5% increments
2protein1drop0.1152ml

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 11.6 Å / Num. obs: 41619 / % possible obs: 94 % / Num. measured all: 137066 / Rmerge(I) obs: 0.06

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→6 Å / σ(F): 1 /
RfactorNum. reflection
obs0.182 38793
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3710 0 20 253 3983
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.016
X-RAY DIFFRACTIONp_angle_d0.0350.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.047
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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