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- PDB-1tre: THE STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE FROM ESCHERICHIA COLI ... -

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Basic information

Entry
Database: PDB / ID: 1tre
TitleTHE STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE FROM ESCHERICHIA COLI DETERMINED AT 2.6 ANGSTROM RESOLUTION
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsINTRAMOLECULAR OXIDOREDUCTASE
Function / homology
Function and homology information


glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / identical protein binding / membrane / 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsNoble, M.E.M. / Wierenga, R.K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Structure of triosephosphate isomerase from Escherichia coli determined at 2.6 A resolution.
Authors: Noble, M.E. / Zeelen, J.P. / Wierenga, R.K. / Mainfroid, V. / Goraj, K. / Gohimont, A.C. / Martial, J.A.
History
DepositionOct 12, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)54,0062
Polymers54,0062
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-15 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.690, 46.780, 151.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTIM IS A DIMERIC ENZYME. THERE IS ONE DIMER IN THE ASYMMETRIC UNIT. CHAIN A CONTAINS RESIDUES 3 - 257 AND CHAIN B CONTAINS RESIDUES 3 - 255.

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE


Mass: 27002.818 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A858, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal grow
*PLUS
Method: vapor diffusion / pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
101 mMdithiothreitol1reservoir
111 mMEDTA1reservoir
121 mM1reservoirNaN3
15 mg/mlprotein1drop
225 mMTris/Hcl1drop
41 mMEDTA1drop
51 mMdithiothreitol1drop
320 mM1dropNaCl
71 mM2-phosphoglycolate1drop
61 mM1dropNaN3
822 %PEG60001reservoir
9200 mMMES1reservoir

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Data collection

DetectorDetector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Num. obs: 12801 / Num. measured all: 51476 / Rmerge(I) obs: 0.083

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.119 / Rfactor obs: 0.119 / Highest resolution: 2.6 Å
Refinement stepCycle: LAST / Highest resolution: 2.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3771 0 0 172 3943
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 2.6 Å / Num. reflection obs: 13812 / Rfactor obs: 0.119 / Lowest resolution: 25 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d

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