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- PDB-5i3f: Structure-Function Studies on Role of Hydrophobic Clamping of a B... -

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Basic information

Entry
Database: PDB / ID: 5i3f
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
Function / homology
Function and homology information


glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / 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
Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)107,2954
Polymers107,2954
Non-polymers00
Water13,151730
1
A: Triosephosphate isomerase, glycosomal
B: Triosephosphate isomerase, glycosomal


Theoretical massNumber of molelcules
Total (without water)53,6482
Polymers53,6482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-20 kcal/mol
Surface area18460 Å2
MethodPISA
2
C: Triosephosphate isomerase, glycosomal
D: Triosephosphate isomerase, glycosomal


Theoretical massNumber of molelcules
Total (without water)53,6482
Polymers53,6482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-20 kcal/mol
Surface area18290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.847, 87.900, 74.848
Angle α, β, γ (deg.)90.00, 106.01, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 730 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20-30% MePEG 5000, 50 mM MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2015 / Details: Rh coated flat mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.718→34.05 Å / Num. obs: 92117 / % possible obs: 98.15 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.14
Reflection shellResolution: 1.718→1.78 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TIM

3tim


Resolution: 1.72→34.05 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 4613 5.02 %
Rwork0.1873 --
obs0.1894 91821 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→34.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7354 0 0 730 8084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067510
X-RAY DIFFRACTIONf_angle_d0.70910214
X-RAY DIFFRACTIONf_dihedral_angle_d12.9634453
X-RAY DIFFRACTIONf_chiral_restr0.0531202
X-RAY DIFFRACTIONf_plane_restr0.0051305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.73960.31051570.24772859X-RAY DIFFRACTION97
1.7396-1.760.34711400.23972867X-RAY DIFFRACTION97
1.76-1.78150.29631600.22792875X-RAY DIFFRACTION98
1.7815-1.8040.30841530.21352880X-RAY DIFFRACTION97
1.804-1.82780.2591460.21022896X-RAY DIFFRACTION98
1.8278-1.85280.2821510.19942865X-RAY DIFFRACTION98
1.8528-1.87930.27061640.20972867X-RAY DIFFRACTION98
1.8793-1.90730.25041600.21122909X-RAY DIFFRACTION98
1.9073-1.93710.32541490.19932836X-RAY DIFFRACTION98
1.9371-1.96890.24141610.2022928X-RAY DIFFRACTION98
1.9689-2.00280.2761420.19532877X-RAY DIFFRACTION98
2.0028-2.03920.23831510.19382917X-RAY DIFFRACTION98
2.0392-2.07850.25471330.19382942X-RAY DIFFRACTION98
2.0785-2.12090.26511300.19852889X-RAY DIFFRACTION98
2.1209-2.1670.24861580.19622941X-RAY DIFFRACTION99
2.167-2.21740.24231730.19362926X-RAY DIFFRACTION99
2.2174-2.27280.23081630.18972880X-RAY DIFFRACTION98
2.2728-2.33430.26191490.19962917X-RAY DIFFRACTION99
2.3343-2.40290.23631650.192912X-RAY DIFFRACTION99
2.4029-2.48050.24271470.18962951X-RAY DIFFRACTION99
2.4805-2.56910.26881410.19732940X-RAY DIFFRACTION99
2.5691-2.67190.2391560.1982923X-RAY DIFFRACTION99
2.6719-2.79350.24571560.19812898X-RAY DIFFRACTION99
2.7935-2.94070.22851680.20192956X-RAY DIFFRACTION99
2.9407-3.12480.20891560.1882943X-RAY DIFFRACTION99
3.1248-3.36590.21661610.18262903X-RAY DIFFRACTION99
3.3659-3.70420.18461560.16572922X-RAY DIFFRACTION98
3.7042-4.23940.16621370.16232890X-RAY DIFFRACTION97
4.2394-5.33780.19221590.16652941X-RAY DIFFRACTION98
5.3378-34.05640.20971710.18162958X-RAY DIFFRACTION97

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