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- PDB-1nf0: Triosephosphate Isomerase in Complex with DHAP -

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Basic information

Entry
Database: PDB / ID: 1nf0
TitleTriosephosphate Isomerase in Complex with DHAP
Componentstriosephosphate isomerase
KeywordsISOMERASE / yeast / triosephosphate isomerase / DHAP / dihydroxyacetone phosphate / michaelis complex
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
1,3-DIHYDROXYACETONEPHOSPHATE / Triosephosphate isomerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / COMO / Resolution: 1.6 Å
AuthorsJogl, G. / Rozovsky, S. / McDermott, A.E. / Tong, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Optimal alignment for enzymatic proton transfer: Structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution
Authors: Jogl, G. / Rozovsky, S. / McDermott, A.E. / Tong, L.
History
DepositionDec 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)53,6444
Polymers53,3042
Non-polymers3402
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-15 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.258, 62.170, 160.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein triosephosphate isomerase / E.C.5.3.1.1 / TIM


Mass: 26652.146 Da / Num. of mol.: 2 / Mutation: W90Y, W157F, W168(FTR)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TPI1 / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JA300 / References: UniProt: P00942, triose-phosphate isomerase
#2: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 277 K / Method: evaporation, recrystallization / pH: 6.8
Details: 50mM TRIS, 50mM NaCl,20% PEG 4000,30mM DHAP, pH 6.8, EVAPORATION, RECRYSTALLIZATION, temperature 277K
Crystal grow
*PLUS
Method: batch method / Details: Rozovsky, S., (2001) J. Mol. Biol., 310, 271.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
140 mg/mlprotein11
250 mMTris-HCl11
350 mM11NaCl
41 mMEDTA11pH6.8
514-16 %PEG400011

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.928 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 4, 2001
RadiationMonochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 62255 / Num. obs: 62255 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.6→1.66 Å / % possible all: 95.5
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. measured all: 231083 / Rmerge(I) obs: 0.065

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
SHELXL-97refinement
RefinementMethod to determine structure: COMO
Starting model: pdb entry 1I45

1i45


Resolution: 1.6→40 Å / Num. parameters: 17233 / Num. restraintsaints: 16005 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST. 28(1995) 53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.268 6291 -RANDOM
Rwork0.209 ---
all0.2091 62255 --
obs0.2091 62255 97.7 %-
Refine analyzeNum. disordered residues: 18 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4194.32
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3865 0 20 419 4304
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.051
X-RAY DIFFRACTIONs_zero_chiral_vol0.047
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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