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- PDB-5zga: Crystal Structure of Triosephosphate isomerase SAD deletion and N... -

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Basic information

Entry
Database: PDB / ID: 5zga
TitleCrystal Structure of Triosephosphate isomerase SAD deletion and N115A 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: 1.793 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 8, 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

Downloads & links

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Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase
C: Triosephosphate isomerase
D: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)118,7684
Polymers118,7684
Non-polymers00
Water18,6091033
1
A: Triosephosphate isomerase
B: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)59,3842
Polymers59,3842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-25 kcal/mol
Surface area19290 Å2
MethodPISA
2
C: Triosephosphate isomerase
D: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)59,3842
Polymers59,3842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-24 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.040, 92.555, 76.075
Angle α, β, γ (deg.)90.000, 109.390, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 5 through 170 or resid 175 through 249))
31chain C
41(chain D and (resid 5 through 170 or resid 175 through 249))

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
11ARGARGchain AAA5 - 24925 - 269
21ARGARG(chain B and (resid 5 through 170 or resid 175 through 249))BB5 - 17025 - 190
22LYSLYS(chain B and (resid 5 through 170 or resid 175 through 249))BB175 - 249195 - 269
31ARGARGchain CCC5 - 24925 - 269
41ARGARG(chain D and (resid 5 through 170 or resid 175 through 249))DD5 - 17025 - 190
42LYSLYS(chain D and (resid 5 through 170 or resid 175 through 249))DD175 - 249195 - 269

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Components

#1: Protein
Triosephosphate isomerase


Mass: 29692.070 Da / Num. of mol.: 4 / Mutation: SAD deletion and N115A
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.: 1033 / 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: 2.07 Å3/Da / Density % sol: 40.59 % / Mosaicity: 0.815 °
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: 1.8→50 Å / Num. obs: 87968 / % possible obs: 97.2 % / Redundancy: 5.3 % / Biso Wilson estimate: 15.92 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.04 / Rrim(I) all: 0.1 / Χ2: 1.857 / Net I/σ(I): 9.6 / Num. measured all: 464383
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8340.27342710.850.1430.311.27195.1
1.83-1.863.90.24642380.8830.1320.2811.19993.7
1.86-1.940.2242200.9330.1140.2491.15193.9
1.9-1.944.60.22143740.940.1090.2471.2997.5
1.94-1.984.70.20144350.9540.0980.2241.44898.2
1.98-2.034.80.18744160.9610.090.2081.47298
2.03-2.084.90.17644110.9650.0840.1961.50297.8
2.08-2.1350.16244150.9730.0760.1791.66698.2
2.13-2.25.10.14744440.9780.0690.1631.71198.3
2.2-2.275.20.13844300.9790.0640.1531.78298
2.27-2.355.20.12443270.9840.0570.1361.68296.1
2.35-2.445.10.11142730.9880.0510.1231.65594.6
2.44-2.555.90.10644970.990.0450.1151.53899.1
2.55-2.6960.09244350.9920.0390.11.46598.7
2.69-2.866.10.0845070.9940.0340.0871.4398.9
2.86-3.086.20.07144730.9960.030.0781.44199
3.08-3.395.90.06243770.9970.0270.0681.60796.7
3.39-3.886.30.06444130.9950.0270.072.18897
3.88-4.886.60.07745060.9940.0320.0843.38698.8
4.88-505.80.09545060.9940.0430.1054.66197.1

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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: 1.793→46.278 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.53 / Phase error: 16.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.181 2012 2.29 %
Rwork0.1466 85911 -
obs0.1474 87923 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.15 Å2 / Biso mean: 21.2706 Å2 / Biso min: 6 Å2
Refinement stepCycle: final / Resolution: 1.793→46.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7542 0 0 1033 8575
Biso mean---32.94 -
Num. residues----972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097688
X-RAY DIFFRACTIONf_angle_d1.10410392
X-RAY DIFFRACTIONf_chiral_restr0.0691164
X-RAY DIFFRACTIONf_plane_restr0.0071338
X-RAY DIFFRACTIONf_dihedral_angle_d19.22856
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4616X-RAY DIFFRACTION7.443TORSIONAL
12B4616X-RAY DIFFRACTION7.443TORSIONAL
13C4616X-RAY DIFFRACTION7.443TORSIONAL
14D4616X-RAY DIFFRACTION7.443TORSIONAL
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 (%)
1.7927-1.83760.22541450.19395758590392
1.8376-1.88720.19221280.17255877600593
1.8872-1.94280.20291450.16376151629697
1.9428-2.00550.18991510.15656181633298
2.0055-2.07720.21931430.15376167631098
2.0772-2.16030.17091370.15156210634798
2.1603-2.25860.19511470.14466184633198
2.2586-2.37770.19011380.14446022616095
2.3777-2.52670.17821490.1476157630698
2.5267-2.72170.18241450.15076264640999
2.7217-2.99560.20711400.15356274641499
2.9956-3.4290.18571460.13726123626997
3.429-4.31960.14541480.12556252640098
4.3196-46.29290.16051500.14546291644197

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