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Basic information

Entry
Database: PDB / ID: 2x16
TitleCrystallographic binding studies with an engineered monomeric variant of triosephosphate isomerase
ComponentsTRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
KeywordsISOMERASE / PENTOSE SHUNT / GLUCONEOGENESIS / LIPID SYNTHESIS / SUBSTRATE SPECIFICITY / FATTY ACID BIOSYNTHESIS / TIM BARREL / PEROXISOME / GLYCOLYSIS / GLYCOSOME
Function / homology
Function and homology information


glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / 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, glycosomal
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsSalin, M. / Kapetaniou, E.G. / Vaismaa, M. / Lajunen, M. / Casteleijn, M.G. / Neubauer, P. / Salmon, L. / Wierenga, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Crystallographic Binding Studies with an Engineered Monomeric Variant of Triosephosphate Isomerase
Authors: Salin, M. / Kapetaniou, E.G. / Vaismaa, M. / Lajunen, M. / Casteleijn, M.G. / Neubauer, P. / Salmon, L. / Wierenga, R.
History
DepositionDec 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references / Other ...Database references / Other / Refinement description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
B: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL


Theoretical massNumber of molelcules
Total (without water)51,3192
Polymers51,3192
Non-polymers00
Water7,206400
1
A: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL


Theoretical massNumber of molelcules
Total (without water)25,6591
Polymers25,6591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL


Theoretical massNumber of molelcules
Total (without water)25,6591
Polymers25,6591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.490, 85.300, 55.880
Angle α, β, γ (deg.)90.00, 98.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL / TIM / TRIOSE-PHOSPHATE ISOMERASE


Mass: 25659.289 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-13,15-72,80-234,238-250 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: A MONOMERIC MUTANT OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE, WHICH HAS AN EMPTY ACTIVE SITE IN BOTH ASYMMETRIC UNITS
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P04789, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 15 TO SER ENGINEERED RESIDUE IN CHAIN A, GLN 18 TO PRO ...ENGINEERED RESIDUE IN CHAIN A, ASN 15 TO SER ENGINEERED RESIDUE IN CHAIN A, GLN 18 TO PRO ENGINEERED RESIDUE IN CHAIN A, GLN 19 TO ASP ENGINEERED RESIDUE IN CHAIN A, ILE 68 TO GLY ENGINEERED RESIDUE IN CHAIN A, ALA 69 TO ASN ENGINEERED RESIDUE IN CHAIN A, LYS 70 TO ALA ENGINEERED RESIDUE IN CHAIN A, SER 71 TO ASP ENGINEERED RESIDUE IN CHAIN A, GLY 72 TO ALA ENGINEERED RESIDUE IN CHAIN A, PRO 81 TO ALA ENGINEERED RESIDUE IN CHAIN A, ILE 82 TO SER ENGINEERED RESIDUE IN CHAIN A, ALA 100 TO TRP ENGINEERED RESIDUE IN CHAIN A, VAL 233 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASN 15 TO SER ENGINEERED RESIDUE IN CHAIN B, GLN 18 TO PRO ENGINEERED RESIDUE IN CHAIN B, GLN 19 TO ASP ENGINEERED RESIDUE IN CHAIN B, ILE 68 TO GLY ENGINEERED RESIDUE IN CHAIN B, ALA 69 TO ASN ENGINEERED RESIDUE IN CHAIN B, LYS 70 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 71 TO ASP ENGINEERED RESIDUE IN CHAIN B, GLY 72 TO ALA ENGINEERED RESIDUE IN CHAIN B, PRO 81 TO ALA ENGINEERED RESIDUE IN CHAIN B, ILE 82 TO SER ENGINEERED RESIDUE IN CHAIN B, ALA 100 TO TRP ENGINEERED RESIDUE IN CHAIN B, VAL 233 TO ALA

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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: 2.24 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 5.5 / Details: 20% PEG6000, 0.1M CITRATE PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8499
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Apr 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8499 Å / Relative weight: 1
ReflectionResolution: 2.13→44.98 Å / Num. obs: 23310 / % possible obs: 98.4 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.3
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VEK

2vek


Resolution: 2.13→44.979 Å / SU ML: 0.34 / σ(F): 2 / Phase error: 26.81 / Stereochemistry target values: ML
Details: RESIDUES 12-19 ARE DISORDERED. DISORDERED REGIONS WERE LEFT OUT FROM THE MODEL.
RfactorNum. reflection% reflection
Rfree0.2608 1161 5 %
Rwork0.1803 --
obs0.1844 23305 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.297 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1-0.6438 Å2-0 Å20.9088 Å2
2--0.808 Å20 Å2
3----1.4517 Å2
Refinement stepCycle: LAST / Resolution: 2.13→44.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 0 400 3893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073575
X-RAY DIFFRACTIONf_angle_d1.054857
X-RAY DIFFRACTIONf_dihedral_angle_d17.1941254
X-RAY DIFFRACTIONf_chiral_restr0.068565
X-RAY DIFFRACTIONf_plane_restr0.004619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.2270.32761310.21772754X-RAY DIFFRACTION98
2.227-2.34440.32791410.21662731X-RAY DIFFRACTION98
2.3444-2.49120.32411530.21322740X-RAY DIFFRACTION98
2.4912-2.68360.28021410.2092781X-RAY DIFFRACTION98
2.6836-2.95360.29011480.18872740X-RAY DIFFRACTION99
2.9536-3.38080.2471470.17952769X-RAY DIFFRACTION99
3.3808-4.2590.2341500.13962806X-RAY DIFFRACTION99
4.259-44.98870.19751500.14722823X-RAY DIFFRACTION99

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