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Basic information

Entry
Database: PDB / ID: 2x1r
TitleCrystallographic binding studies with an engineered monomeric variant of triosephosphate isomerase
ComponentsTRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
KeywordsISOMERASE / GLUCONEOGENESIS / LIPID SYNTHESIS / 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
3-(PROPYLSULFONYL)PROPANOIC ACID / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / 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)51,9677
Polymers51,3192
Non-polymers6495
Water9,278515
1
A: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9363
Polymers25,6591
Non-polymers2762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0324
Polymers25,6591
Non-polymers3723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.940, 86.920, 56.280
Angle α, β, γ (deg.)90.00, 98.58, 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 A BOUND 3-(PROPYLSULPHONYL)PROPIONIC ACID (X1R) LIGAND 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-X1R / 3-(PROPYLSULFONYL)PROPANOIC ACID


Mass: 180.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8499 Å / Relative weight: 1
ReflectionResolution: 1.97→45.46 Å / Num. obs: 28367 / % possible obs: 91.4 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Biso Wilson estimate: 18.63 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.1
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3 / % possible all: 85.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.5_2)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VEK

2vek


Resolution: 1.98→14.92 Å / SU ML: 0.26 / σ(F): 1.99 / Phase error: 21.95 / Stereochemistry target values: ML / Details: RESIDUES 13-19 IN MOLECULE A ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.226 1400 5 %
Rwork0.161 --
obs0.164 27986 92.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.84 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 19 Å2
Baniso -1Baniso -2Baniso -3
1-1.4175 Å20 Å22.2096 Å2
2--0.7434 Å20 Å2
3----2.1609 Å2
Refinement stepCycle: LAST / Resolution: 1.98→14.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3577 0 37 515 4129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073690
X-RAY DIFFRACTIONf_angle_d1.0025015
X-RAY DIFFRACTIONf_dihedral_angle_d16.7441301
X-RAY DIFFRACTIONf_chiral_restr0.068577
X-RAY DIFFRACTIONf_plane_restr0.004636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9803-2.05090.29561470.20622792X-RAY DIFFRACTION98
2.0509-2.13270.25561500.18332864X-RAY DIFFRACTION100
2.1327-2.22950.26381370.17042585X-RAY DIFFRACTION98
2.2295-2.34660.2315800.16981503X-RAY DIFFRACTION95
2.3466-2.4930.23861510.15962873X-RAY DIFFRACTION100
2.493-2.68450.21691530.16322884X-RAY DIFFRACTION100
2.6845-2.95270.22621520.16522888X-RAY DIFFRACTION100
2.9527-3.37570.21621500.1582869X-RAY DIFFRACTION100
3.3757-4.23680.21651260.14132395X-RAY DIFFRACTION82
4.2368-14.91760.1881540.14292933X-RAY DIFFRACTION100

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