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- PDB-5zg5: Crystal Structure of Triosephosphate isomerase SADsubAAA mutant f... -

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Basic information

Entry
Database: PDB / ID: 5zg5
TitleCrystal Structure of Triosephosphate isomerase SADsubAAA mutant from Opisthorchis viverrini
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / Tim-barrel / Triosephosphate isomerase
Function / homology
Function and homology information


glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / metal ion binding / cytosol
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: 1.597 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)59,8972
Polymers59,8972
Non-polymers00
Water11,908661
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-24 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.840, 90.369, 102.265
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 5 - 252 / Label seq-ID: 25 - 272

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Triosephosphate isomerase


Mass: 29948.330 Da / Num. of mol.: 2 / Mutation: SADsubAAA mutant
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.66 Å3/Da / Density % sol: 53.68 % / Mosaicity: 0.62 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5 / Details: PEG 3350

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 82985 / % possible obs: 98.7 % / Redundancy: 7.9 % / Biso Wilson estimate: 13.41 Å2 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.057 / Rrim(I) all: 0.178 / Χ2: 1.627 / Net I/σ(I): 5.3 / Num. measured all: 654169
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.58-1.614.50.47339200.4320.2340.5320.73395.3
1.61-1.644.90.47140500.5440.2210.5240.8196.9
1.64-1.675.30.46640210.560.2120.5150.77897.6
1.67-1.75.60.4640700.6560.2030.5060.80897.9
1.7-1.745.70.44841290.6730.1950.4910.85598.7
1.74-1.785.70.42440590.7240.1830.4640.91298.3
1.78-1.826.60.39841160.7950.1570.4290.96898.6
1.82-1.877.20.40141380.8440.1520.431.02199.2
1.87-1.937.70.38241430.8780.1410.4091.16399.4
1.93-1.9980.35441430.9060.1280.3781.34199.4
1.99-2.068.10.33241770.9130.1190.3541.41899.3
2.06-2.147.80.29541400.9370.1080.3141.5399.4
2.14-2.249.10.27241510.9470.0920.2881.54199.6
2.24-2.369.70.2441990.9710.0780.2531.58299.5
2.36-2.519.80.21541790.9740.070.2271.57999.6
2.51-2.79.70.18641900.9820.0610.1961.67499.3
2.7-2.979.90.15341890.9890.0490.1621.73798.9
2.97-3.410.90.1242620.9940.0370.1262.0299.6
3.4-4.2910.30.10242600.9950.0320.1072.55899.1
4.29-5010.40.12344490.9940.0390.1293.82698.8

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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: 5ZFX

5zfx


Resolution: 1.597→48.276 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 17.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.195 1999 2.41 %
Rwork0.1706 80916 -
obs0.1711 82915 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.71 Å2 / Biso mean: 18.4694 Å2 / Biso min: 6.71 Å2
Refinement stepCycle: final / Resolution: 1.597→48.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3830 0 0 661 4491
Biso mean---32.96 -
Num. residues----496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073904
X-RAY DIFFRACTIONf_angle_d0.9375280
X-RAY DIFFRACTIONf_chiral_restr0.058592
X-RAY DIFFRACTIONf_plane_restr0.006682
X-RAY DIFFRACTIONf_dihedral_angle_d16.4931446
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2324X-RAY DIFFRACTION2.54TORSIONAL
12B2324X-RAY DIFFRACTION2.54TORSIONAL
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 (%)
1.5969-1.63680.30661090.25224400450975
1.6368-1.68110.28441420.23985767590997
1.6811-1.73060.26171420.23095714585698
1.7306-1.78640.22471430.22515806594999
1.7864-1.85030.23281430.20175787593098
1.8503-1.92440.21381450.19785854599999
1.9244-2.01190.21351450.18185876602199
2.0119-2.1180.22381450.18145832597799
2.118-2.25070.21041440.16695903604799
2.2507-2.42450.16781470.156559226069100
2.4245-2.66840.17411460.15665909605599
2.6684-3.05450.20181460.15835936608299
3.0545-3.84810.1541480.143660196167100
3.8481-48.29760.16761540.15126191634599

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