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- PDB-5i3g: Structure-Function Studies on Role of Hydrophobic Clamping of a B... -

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Basic information

Entry
Database: PDB / ID: 5i3g
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 / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / 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
Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 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


Theoretical massNumber of molelcules
Total (without water)107,1274
Polymers107,1274
Non-polymers00
Water18,8261045
1
A: Triosephosphate isomerase, glycosomal
C: Triosephosphate isomerase, glycosomal


Theoretical massNumber of molelcules
Total (without water)53,5632
Polymers53,5632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-21 kcal/mol
Surface area19000 Å2
MethodPISA
2
B: Triosephosphate isomerase, glycosomal
D: Triosephosphate isomerase, glycosomal


Theoretical massNumber of molelcules
Total (without water)53,5632
Polymers53,5632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-21 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.420, 75.416, 75.779
Angle α, β, γ (deg.)102.04, 104.78, 97.84
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 26781.672 Da / Num. of mol.: 4 / Mutation: I172A,L232A
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.: 1045 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15-25% Peg 8000, 50-100 mM potassium acetate, 100 mM BTP pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→29.03 Å / Num. obs: 67582 / % possible obs: 98.87 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 7
Reflection shellResolution: 1.96→2.03 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TIM

3tim


Resolution: 1.96→29.03 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 26.13
RfactorNum. reflection% reflection
Rfree0.2216 3411 5.06 %
Rwork0.1725 --
obs0.1749 67473 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→29.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7428 0 0 1045 8473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087604
X-RAY DIFFRACTIONf_angle_d0.83510336
X-RAY DIFFRACTIONf_dihedral_angle_d13.7694524
X-RAY DIFFRACTIONf_chiral_restr0.0551208
X-RAY DIFFRACTIONf_plane_restr0.0051323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.9880.3441320.24442487X-RAY DIFFRACTION91
1.988-2.01770.28911470.20862657X-RAY DIFFRACTION99
2.0177-2.04920.22441520.19242638X-RAY DIFFRACTION99
2.0492-2.08280.26531640.1762663X-RAY DIFFRACTION99
2.0828-2.11870.23771470.17662678X-RAY DIFFRACTION99
2.1187-2.15720.23571530.17742669X-RAY DIFFRACTION99
2.1572-2.19870.23341300.17282696X-RAY DIFFRACTION99
2.1987-2.24360.23641330.17712676X-RAY DIFFRACTION99
2.2436-2.29230.24781310.17812733X-RAY DIFFRACTION99
2.2923-2.34560.31071140.18652691X-RAY DIFFRACTION99
2.3456-2.40430.24351470.17932686X-RAY DIFFRACTION99
2.4043-2.46920.23861590.17662668X-RAY DIFFRACTION99
2.4692-2.54180.23261450.17642681X-RAY DIFFRACTION99
2.5418-2.62380.23691440.17852698X-RAY DIFFRACTION100
2.6238-2.71750.21481480.17192717X-RAY DIFFRACTION100
2.7175-2.82630.24561480.17942656X-RAY DIFFRACTION100
2.8263-2.95480.20481260.17852711X-RAY DIFFRACTION100
2.9548-3.11040.23371490.17332707X-RAY DIFFRACTION100
3.1104-3.3050.20181550.16882703X-RAY DIFFRACTION100
3.305-3.55980.19481390.16152702X-RAY DIFFRACTION100
3.5598-3.91720.20021350.15112675X-RAY DIFFRACTION99
3.9172-4.48230.18921350.14692665X-RAY DIFFRACTION99
4.4823-5.64040.18091320.16162681X-RAY DIFFRACTION98
5.6404-29.0350.17461460.17632524X-RAY DIFFRACTION94

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