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- PDB-5i3i: Structure-Function Studies on Role of Hydrophobic Clamping of a B... -

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Basic information

Entry
Database: PDB / ID: 5i3i
TitleStructure-Function Studies on Role of Hydrophobic Clamping of a Basic Glutamate in Catalysis by Triosephosphate Isomerase
ComponentsTriosephosphate isomerase, glycosomal
KeywordsISOMERASE / Triosephosphate Isomerase / Catalysis / Hydrophobic Clamping / PGA
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
2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDrake, E.J. / Gulick, A.M. / Richard, J.P. / Zhai, X. / Kim, K. / Reinhardt, C.J.
CitationJournal: Biochemistry / Year: 2016
Title: Structure-Function Studies of Hydrophobic Residues That Clamp a Basic Glutamate Side Chain during Catalysis by Triosephosphate Isomerase.
Authors: Richard, J.P. / Amyes, T.L. / Malabanan, M.M. / Zhai, X. / Kim, K.J. / Reinhardt, C.J. / Wierenga, R.K. / Drake, E.J. / Gulick, A.M.
History
DepositionFeb 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Triosephosphate isomerase, glycosomal
B: Triosephosphate isomerase, glycosomal
C: Triosephosphate isomerase, glycosomal
D: Triosephosphate isomerase, glycosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9198
Polymers107,2954
Non-polymers6244
Water6,539363
1
A: Triosephosphate isomerase, glycosomal
B: Triosephosphate isomerase, glycosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9604
Polymers53,6482
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-31 kcal/mol
Surface area18220 Å2
MethodPISA
2
C: Triosephosphate isomerase, glycosomal
D: Triosephosphate isomerase, glycosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9604
Polymers53,6482
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-32 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.730, 87.500, 76.300
Angle α, β, γ (deg.)90.00, 107.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Triosephosphate isomerase, glycosomal / Triose-phosphate isomerase


Mass: 26823.752 Da / Num. of mol.: 4 / Mutation: I172A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: P04789, triose-phosphate isomerase
#2: Chemical
ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20-30% MePEG 5000, 2-4% PEP, 50 mM MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.284 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 6, 2012 / Details: Rh coated flat mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.284 Å / Relative weight: 1
ReflectionResolution: 2.2→58.57 Å / Num. obs: 42618 / % possible obs: 95.69 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.0581 / Net I/σ(I): 7.53
Reflection shellResolution: 2.2→2.279 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TIM

3tim


Resolution: 2.2→58.57 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.61
RfactorNum. reflection% reflection
Rfree0.2494 2175 5.11 %
Rwork0.2029 --
obs0.2053 42593 95.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→58.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7423 0 36 363 7822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027591
X-RAY DIFFRACTIONf_angle_d0.57510321
X-RAY DIFFRACTIONf_dihedral_angle_d12.9912657
X-RAY DIFFRACTIONf_chiral_restr0.0211208
X-RAY DIFFRACTIONf_plane_restr0.0031318
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.24780.31731310.272229887
2.2478-2.30010.3391390.2675250296
2.3001-2.35770.3141400.2589252696
2.3577-2.42140.33811330.2564255496
2.4214-2.49270.29881230.2467255097
2.4927-2.57310.29281520.2399254096
2.5731-2.66510.31391230.237252796
2.6651-2.77180.32791310.2438255597
2.7718-2.89790.33111330.2333255297
2.8979-3.05070.25071390.2236256097
3.0507-3.24180.2421280.2119255797
3.2418-3.49210.2661290.2025259297
3.4921-3.84350.19191350.1752254597
3.8435-4.39950.22821500.1629252296
4.3995-5.54220.18711280.1651250193
5.54220.19321610.1575253794

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