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Basic information

Entry
Database: PDB / ID: 2x1t
TitleCrystallographic binding studies with an engineered monomeric variant of triosephosphate isomerase
ComponentsTRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
KeywordsISOMERASE / FATTY ACID BIOSYNTHESIS / GLUCONEOGENESIS / GLYCOLYSIS / GLYCOSOME / LIPID SYNTHESIS
Function / homology
Function and homology information


glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / 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
4-PHOSPHO-D-ERYTHRONOHYDROXAMIC ACID / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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
DepositionJan 4, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references / 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5503
Polymers51,3192
Non-polymers2311
Water10,899605
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8902
Polymers25,6591
Non-polymers2311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.640, 86.850, 55.880
Angle α, β, γ (deg.)90.00, 97.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL / TRIOSEPHOSPHATE ISOMERASE / TIM


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: Chemical ChemComp-RES / 4-PHOSPHO-D-ERYTHRONOHYDROXAMIC ACID


Mass: 231.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10NO8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / 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: X12 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→46.7 Å / Num. obs: 38001 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 15.72 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.4
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3 / % possible all: 99.6

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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: 1.83→26.4 Å / SU ML: 0.22 / σ(F): 1.99 / Phase error: 21.39 / Stereochemistry target values: ML / Details: RESIDUES 14-19 IN MOLECULE A ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2194 1898 5 %
Rwork0.1716 --
obs0.1741 37993 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.919 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso mean: 16 Å2
Baniso -1Baniso -2Baniso -3
1-0.0861 Å20 Å20.059 Å2
2--0.7545 Å20 Å2
3----0.8406 Å2
Refinement stepCycle: LAST / Resolution: 1.83→26.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3587 0 14 605 4206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073672
X-RAY DIFFRACTIONf_angle_d1.0154988
X-RAY DIFFRACTIONf_dihedral_angle_d16.6051295
X-RAY DIFFRACTIONf_chiral_restr0.068577
X-RAY DIFFRACTIONf_plane_restr0.004634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.87580.28441350.22112533X-RAY DIFFRACTION99
1.8758-1.92650.24851370.19852580X-RAY DIFFRACTION100
1.9265-1.98320.25871370.1822586X-RAY DIFFRACTION100
1.9832-2.04710.24451290.17932540X-RAY DIFFRACTION100
2.0471-2.12030.25271390.17662556X-RAY DIFFRACTION100
2.1203-2.20510.24591320.17672574X-RAY DIFFRACTION100
2.2051-2.30540.19441350.1662588X-RAY DIFFRACTION100
2.3054-2.42690.24131330.16152582X-RAY DIFFRACTION100
2.4269-2.57880.22141360.17112579X-RAY DIFFRACTION100
2.5788-2.77780.1971360.17612565X-RAY DIFFRACTION100
2.7778-3.05690.23951370.16932614X-RAY DIFFRACTION100
3.0569-3.49840.2051350.16812587X-RAY DIFFRACTION100
3.4984-4.40430.18711360.14732575X-RAY DIFFRACTION100
4.4043-26.40320.19411410.17012636X-RAY DIFFRACTION100

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