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- PDB-7tim: STRUCTURE OF THE TRIOSEPHOSPHATE ISOMERASE-PHOSPHOGLYCOLOHYDROXAM... -

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Basic information

Entry
Database: PDB / ID: 7tim
TitleSTRUCTURE OF THE TRIOSEPHOSPHATE ISOMERASE-PHOSPHOGLYCOLOHYDROXAMATE COMPLEX: AN ANALOGUE OF THE INTERMEDIATE ON THE REACTION PATHWAY
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsINTRAMOLECULAR OXIDOREDUCTASE
Function / homology
Function and homology information


Gluconeogenesis / Glycolysis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / mitochondrion / plasma membrane ...Gluconeogenesis / Glycolysis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / mitochondrion / plasma membrane / cytosol / cytoplasm
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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsDavenport, R.C. / Bash, P.A. / Seaton, B.A. / Karplus, M. / Petsko, G.A. / Ringe, D.
CitationJournal: Biochemistry / Year: 1991
Title: Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: an analogue of the intermediate on the reaction pathway.
Authors: Davenport, R.C. / Bash, P.A. / Seaton, B.A. / Karplus, M. / Petsko, G.A. / Ringe, D.
History
DepositionApr 23, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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_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_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)53,7354
Polymers53,3922
Non-polymers3422
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-21 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.000, 83.500, 38.400
Angle α, β, γ (deg.)90.00, 99.55, 90.00
Int Tables number4
Space group name H-MP1211

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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: 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.: 247 / 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: 2.19 Å3/Da / Density % sol: 43.85 %

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.183 / Rfactor obs: 0.183 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 20 247 4033
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 3 Å / Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS

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