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- PDB-5zfx: Crystal Structure of Triosephosphate isomerase from Opisthorchis ... -

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Basic information

Entry
Database: PDB / ID: 5zfx
TitleCrystal Structure of Triosephosphate isomerase from Opisthorchis viverrini
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / Tim-barrel / Triosephosphate isomerase
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process
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
Similarity search - Component
Biological speciesOpisthorchis viverrini (Southeast Asian liver fluke)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.751 Å
AuthorsSon, J. / Kim, S. / Kim, S.E. / Lee, H. / Lee, M.R. / Hwang, K.Y.
CitationJournal: Sci Rep / Year: 2018
Title: Structural Analysis of an Epitope Candidate of Triosephosphate Isomerase in Opisthorchis viverrini.
Authors: Son, J. / Kim, S. / Kim, S.E. / Lee, H. / Lee, M.R. / Hwang, K.Y.
History
DepositionMar 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
B: Triosephosphate isomerase
C: Triosephosphate isomerase
D: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,0826
Polymers120,0334
Non-polymers492
Water21,5281195
1
A: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0654
Polymers60,0172
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-38 kcal/mol
Surface area19380 Å2
MethodPISA
2
C: Triosephosphate isomerase
D: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)60,0172
Polymers60,0172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-25 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.529, 206.621, 97.466
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 173 or resid 179 through 252))
21(chain B and (resid 5 through 173 or resid 179 through 252))
31chain C
41chain D

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: ALA / End label comp-ID: ALA

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARG(chain A and (resid 5 through 173 or resid 179 through 252))AA5 - 17325 - 193
12THRTHR(chain A and (resid 5 through 173 or resid 179 through 252))AA179 - 252199 - 272
21ARGARG(chain B and (resid 5 through 173 or resid 179 through 252))BB5 - 17325 - 193
22THRTHR(chain B and (resid 5 through 173 or resid 179 through 252))BB179 - 252199 - 272
31ARGARGchain CCC5 - 25225 - 272
41ARGARGchain DDD5 - 25225 - 272

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Components

#1: Protein
Triosephosphate isomerase /


Mass: 30008.338 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Opisthorchis viverrini (Southeast Asian liver fluke)
Gene: T265_10017 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A074Z863, triose-phosphate isomerase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1195 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence conflicts may be resulted from the difference of subspecies of the source organism.

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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: 2.22 Å3/Da / Density % sol: 39.6 % / Mosaicity: 0.508 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5 / Details: PEG 3350

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00001 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 96825 / % possible obs: 98.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 15.65 Å2 / Rmerge(I) obs: 0.105 / Χ2: 11.73 / Net I/σ(I): 37.7 / Num. measured all: 541897
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.75-1.813.10.1190524.923193.3
1.81-1.893.90.09995414.681198.5
1.89-1.974.10.08496074.775198.6
1.97-2.074.30.07396514.837199.2
2.07-2.24.40.06596914.82199.6
2.2-2.384.60.0697274.925199.6
2.38-2.614.60.05797295.122199.6
2.61-2.998.40.144981318.337199.9
2.99-3.779.30.099988713.8471100
3.77-508.70.1141012721.961199.6

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TPH

1tph


Resolution: 1.751→44.075 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.56 / Phase error: 18.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2004 2000 2.07 %
Rwork0.164 94809 -
obs0.1648 96809 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.76 Å2 / Biso mean: 21.1921 Å2 / Biso min: 5.06 Å2
Refinement stepCycle: final / Resolution: 1.751→44.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7589 0 2 1195 8786
Biso mean--24.8 34.45 -
Num. residues----978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077734
X-RAY DIFFRACTIONf_angle_d0.92910456
X-RAY DIFFRACTIONf_chiral_restr0.0621170
X-RAY DIFFRACTIONf_plane_restr0.0061351
X-RAY DIFFRACTIONf_dihedral_angle_d18.3022870
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4628X-RAY DIFFRACTION6.27TORSIONAL
12B4628X-RAY DIFFRACTION6.27TORSIONAL
13C4628X-RAY DIFFRACTION6.27TORSIONAL
14D4628X-RAY DIFFRACTION6.27TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7506-1.79440.2231300.18656171630191
1.7944-1.84290.20911410.18056656679798
1.8429-1.89720.22731410.17176707684898
1.8972-1.95840.23581410.17136685682699
1.9584-2.02840.20031430.17016759690299
2.0284-2.10960.2051430.17556770691399
2.1096-2.20560.21461420.162667806922100
2.2056-2.32190.2111440.164767926936100
2.3219-2.46740.22141430.170367976940100
2.4674-2.65780.19851440.172368546998100
2.6578-2.92530.20781450.175268697014100
2.9253-3.34840.20611460.165569007046100
3.3484-4.21810.16821470.141669437090100
4.2181-44.08930.18781500.15677126727699

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