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- PDB-1kv5: Structure of Trypanosoma brucei brucei TIM with the salt-bridge-f... -

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Basic information

Entry
Database: PDB / ID: 1kv5
TitleStructure of Trypanosoma brucei brucei TIM with the salt-bridge-forming residue Arg191 mutated to Ser
Componentstriosephosphate isomerase, glycosomal
KeywordsISOMERASE / TIM barrel / mutant / salt bridge
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / 2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKursula, I. / Partanen, S. / Lambeir, A.-M. / Wierenga, R.K.
CitationJournal: FEBS Lett. / Year: 2002
Title: The importance of the conserved Arg191-Asp227 salt bridge of triosephosphate isomerase for folding, stability, and catalysis
Authors: Kursula, I. / Partanen, S. / Lambeir, A.-M. / Wierenga, R.K.
History
DepositionJan 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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, glycosomal
B: triosephosphate isomerase, glycosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,52210
Polymers53,5912
Non-polymers9318
Water14,034779
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-50 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.943, 100.638, 109.350
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

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Protein , 1 types, 2 molecules AB

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


Mass: 26795.717 Da / Num. of mol.: 2 / Mutation: R191S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Species: Trypanosoma brucei / Strain: brucei / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04789, triose-phosphate isomerase

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Non-polymers , 5 types, 787 molecules

#2: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 779 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulfate, sodium chloride, citric acid, pH 5.5, VAPOR DIFFUSION, HANGING DROP at 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 Mammonium sulfate1reservoir
20.1 Mcitric acid1reservoirpH5.5
30.2 M1reservoirNaCl
43 mg/mlprotein1drop
510 mMPGA1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.85 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 27, 2001
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.65→15 Å / Num. all: 115031 / Num. obs: 115031 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 37.7
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 5.4 / % possible all: 99.3
Reflection
*PLUS
Lowest resolution: 15 Å / Num. obs: 60451 / Num. measured all: 245458
Reflection shell
*PLUS
% possible obs: 99.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5TIM

5tim


Resolution: 1.65→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.17539 3053 5.1 %RANDOM
Rwork0.14292 ---
obs0.14454 57315 99.9 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK PARAMETERS FOR MASK CALCULATION
Displacement parametersBiso mean: 15.469 Å2
Refinement stepCycle: LAST / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3756 0 55 779 4590
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.0130
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.9
X-RAY DIFFRACTIONr_mcbond_it0.8491.5
X-RAY DIFFRACTIONr_mcangle_it1.5342
X-RAY DIFFRACTIONr_scbond_it2.4293
X-RAY DIFFRACTIONr_scangle_it3.9134.5
LS refinement shellHighest resolution: 1.65 Å / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.172 / Total num. of bins used: 20
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor obs: 0.143 / Rfactor Rfree: 0.175 / Rfactor Rwork: 0.143
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.77

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