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- PDB-6oog: Crystal structure of triosephosphate isomerase from Taenia Solium... -

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Basic information

Entry
Database: PDB / ID: 6oog
TitleCrystal structure of triosephosphate isomerase from Taenia Solium in complex with 2PG
ComponentsTriosephosphate isomerase
KeywordsISOMERASE
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / 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
Similarity search - Component
Biological speciesTaenia solium (pork tapeworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 Å
AuthorsJimenez-Sandoval, P. / Brieba, L.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)Fronteras de la Ciencia 13 Mexico
CitationJournal: Plos Negl Trop Dis / Year: 2020
Title: Crystal structures of Triosephosphate Isomerases from Taenia solium and Schistosoma mansoni provide insights for vaccine rationale and drug design against helminth parasites.
Authors: Jimenez-Sandoval, P. / Castro-Torres, E. / Gonzalez-Gonzalez, R. / Diaz-Quezada, C. / Gurrola, M. / Camacho-Manriquez, L.D. / Leyva-Navarro, L. / Brieba, L.G.
History
DepositionApr 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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
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.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6743
Polymers27,4951
Non-polymers1792
Water3,405189
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3496
Polymers54,9912
Non-polymers3584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4000 Å2
ΔGint-53 kcal/mol
Surface area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.370, 66.370, 155.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Triosephosphate isomerase / TIM / Triose-phosphate isomerase


Mass: 27495.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Taenia solium (pork tapeworm) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9GTX8, triose-phosphate isomerase
#2: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.12 Å3/Da / Density % sol: 60.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium acetate trihydrate 0.1M Sodium cacodylate trihydrate 6.5 30% w/v Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.5419 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.02→61.044 Å / Num. obs: 23571 / % possible obs: 99.7 % / Redundancy: 10.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.298 / Rpim(I) all: 0.095 / Rrim(I) all: 0.314 / Net I/σ(I): 7.2
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 9.8 % / Rmerge(I) obs: 2.307 / Num. measured all: 16512 / Num. unique obs: 1693 / CC1/2: 0.339 / Rpim(I) all: 0.757 / Rrim(I) all: 2.433 / Net I/σ(I) obs: 1.2 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.96 Å61.05 Å
Translation5.96 Å61.05 Å

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
PHASER2.8.1phasing
PDB_EXTRACT3.25data extraction
CrystalCleardata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TH6

3th6


Resolution: 2.02→61.044 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.97
RfactorNum. reflection% reflection
Rfree0.2243 1177 5 %
Rwork0.1842 --
obs0.1863 23526 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.49 Å2 / Biso mean: 25.6229 Å2 / Biso min: 13.17 Å2
Refinement stepCycle: final / Resolution: 2.02→61.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 10 189 2083
Biso mean--22.35 30.59 -
Num. residues----252
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0201-2.11210.32171420.2946270699
2.1121-2.22340.28511430.2542271899
2.2234-2.36270.24441450.2279274499
2.3627-2.54520.27921450.2172751100
2.5452-2.80130.25881450.19792769100
2.8013-3.20660.24351470.18782794100
3.2066-4.03990.18231500.14442846100
4.0399-61.0440.17711600.15043021100

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