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- PDB-5i3j: Structure-Function Studies on Role of Hydrophobic Clamping of a B... -

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Basic information

Entry
Database: PDB / ID: 5i3j
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 / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / 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_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7396
Polymers53,6482
Non-polymers924
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-58 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.030, 44.120, 71.700
Angle α, β, γ (deg.)79.06, 77.49, 63.11
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 26823.752 Da / Num. of mol.: 2 / 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.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.04 Å3/Da / Density % sol: 39.72 %
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: 1.8→35.3 Å / Num. obs: 36591 / % possible obs: 92.85 % / Redundancy: 2 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.41
Reflection shellResolution: 1.8→1.864 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: 1.8→35.3 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.85
RfactorNum. reflection% reflection
Rfree0.2106 1946 5.32 %
Rwork0.1634 --
obs0.166 36573 92.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→35.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3693 0 4 561 4258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173807
X-RAY DIFFRACTIONf_angle_d0.655171
X-RAY DIFFRACTIONf_dihedral_angle_d12.3782250
X-RAY DIFFRACTIONf_chiral_restr0.049610
X-RAY DIFFRACTIONf_plane_restr0.004665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.30241370.24812485X-RAY DIFFRACTION92
1.845-1.89490.30071200.21862458X-RAY DIFFRACTION92
1.8949-1.95070.20881390.19612418X-RAY DIFFRACTION92
1.9507-2.01360.24591340.18752493X-RAY DIFFRACTION92
2.0136-2.08560.21971290.17612441X-RAY DIFFRACTION92
2.0856-2.16910.22051580.16472444X-RAY DIFFRACTION92
2.1691-2.26780.20771350.16222462X-RAY DIFFRACTION93
2.2678-2.38730.23551300.15942553X-RAY DIFFRACTION94
2.3873-2.53680.23951420.1572449X-RAY DIFFRACTION93
2.5368-2.73260.18961440.16052469X-RAY DIFFRACTION93
2.7326-3.00750.19351500.16352449X-RAY DIFFRACTION93
3.0075-3.44240.19011400.15012481X-RAY DIFFRACTION93
3.4424-4.33580.20471240.13482402X-RAY DIFFRACTION90
4.3358-35.30810.17021640.15082623X-RAY DIFFRACTION99

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