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- PDB-5i3k: Structure-Function Studies on Role of Hydrophobic Clamping of a B... -

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Basic information

Entry
Database: PDB / ID: 5i3k
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 / 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
2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.209 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_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,83210
Polymers107,2954
Non-polymers5376
Water6,810378
1
A: Triosephosphate isomerase, glycosomal
D: Triosephosphate isomerase, glycosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8505
Polymers53,6482
Non-polymers2023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-35 kcal/mol
Surface area18210 Å2
MethodPISA
2
B: Triosephosphate isomerase, glycosomal
C: Triosephosphate isomerase, glycosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9835
Polymers53,6482
Non-polymers3353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-44 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.890, 87.600, 76.380
Angle α, β, γ (deg.)90.00, 107.35, 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: 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


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


Mass: 18.015 Da / Num. of mol.: 378 / 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: 40.77 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20-30% Peg 4000, 150-250 mM NaCl, 50 mM Epps

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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: May 21, 2015 / 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: 2.209→72.91 Å / Num. obs: 43105 / % possible obs: 97.53 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 7.45
Reflection shellResolution: 2.209→2.288 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TIM

3tim


Resolution: 2.209→72.91 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.54
RfactorNum. reflection% reflection
Rfree0.2644 2238 5.19 %
Rwork0.219 --
obs0.2213 43087 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.209→72.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7293 0 30 378 7701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037460
X-RAY DIFFRACTIONf_angle_d0.43110162
X-RAY DIFFRACTIONf_dihedral_angle_d11.6254378
X-RAY DIFFRACTIONf_chiral_restr0.0431207
X-RAY DIFFRACTIONf_plane_restr0.0031300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.209-2.25710.33911410.26812581X-RAY DIFFRACTION99
2.2571-2.30960.31671320.27662597X-RAY DIFFRACTION99
2.3096-2.36740.38271280.26862592X-RAY DIFFRACTION99
2.3674-2.43140.31361320.26112591X-RAY DIFFRACTION99
2.4314-2.50290.32931540.25732570X-RAY DIFFRACTION99
2.5029-2.58370.33261350.24742614X-RAY DIFFRACTION99
2.5837-2.67610.29271540.24552556X-RAY DIFFRACTION99
2.6761-2.78320.27341270.23522588X-RAY DIFFRACTION99
2.7832-2.90990.30071620.23752570X-RAY DIFFRACTION99
2.9099-3.06330.32091330.23222575X-RAY DIFFRACTION99
3.0633-3.25520.24711550.2222548X-RAY DIFFRACTION98
3.2552-3.50650.28771270.21632579X-RAY DIFFRACTION97
3.5065-3.85940.24281320.19762535X-RAY DIFFRACTION97
3.8594-4.41780.22331160.18112527X-RAY DIFFRACTION96
4.4178-5.56570.20711480.18612396X-RAY DIFFRACTION91
5.5657-72.94450.21521620.20362430X-RAY DIFFRACTION91

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