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- PDB-6ooi: Crystal structure of triosephosphate isomerase from Schistosoma m... -

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Basic information

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


triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / 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
2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase
C: Triosephosphate isomerase
D: Triosephosphate isomerase
E: Triosephosphate isomerase
F: Triosephosphate isomerase
G: Triosephosphate isomerase
H: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,48132
Polymers227,6528
Non-polymers1,82924
Water19,3661075
1
A: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3659
Polymers56,9132
Non-polymers4527
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-81 kcal/mol
Surface area19130 Å2
MethodPISA
2
C: Triosephosphate isomerase
D: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4349
Polymers56,9132
Non-polymers5217
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-73 kcal/mol
Surface area19670 Å2
MethodPISA
3
E: Triosephosphate isomerase
F: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3067
Polymers56,9132
Non-polymers3935
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-59 kcal/mol
Surface area19100 Å2
MethodPISA
4
G: Triosephosphate isomerase
H: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3767
Polymers56,9132
Non-polymers4635
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-51 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.050, 108.050, 182.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 28456.465 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: TPI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P48501, triose-phosphate isomerase

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Non-polymers , 5 types, 1099 molecules

#2: Chemical
ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H5O6P
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1075 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M Cesium chloride 0.1M MES monohydrate 6.5 30% v/v Jeffamine M-600

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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 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.14→58.61 Å / Num. obs: 115018 / % possible obs: 100 % / Redundancy: 4.5 % / CC1/2: 0.984 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.081 / Rrim(I) all: 0.173 / Net I/σ(I): 5.6 / Num. measured all: 517652 / Scaling rejects: 76
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.804 / Num. measured all: 24134 / Num. unique obs: 5688 / CC1/2: 0.639 / Rpim(I) all: 0.436 / Rrim(I) all: 0.917 / Net I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
CrystalCleardata collection
Cootmodel building
Aimlessdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZFX

5zfx


Resolution: 2.14→58.609 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 2015 1.75 %
Rwork0.1805 112898 -
obs0.1814 114913 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.04 Å2 / Biso mean: 24.1252 Å2 / Biso min: 7.17 Å2
Refinement stepCycle: final / Resolution: 2.14→58.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15115 0 98 1075 16288
Biso mean--22.74 24.06 -
Num. residues----2003
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 (%)
2.14-2.19350.29051400.222180418181100
2.1935-2.25290.26061480.211880568204100
2.2529-2.31910.24731440.194280278171100
2.3191-2.3940.23391440.195680888232100
2.394-2.47960.25131420.197180148156100
2.4796-2.57880.26321460.198980298175100
2.5788-2.69620.25391430.200980808223100
2.6962-2.83840.27711470.208580798226100
2.8384-3.01620.28061470.201380378184100
3.0162-3.2490.24871390.194880618200100
3.249-3.5760.22451430.180280688211100
3.576-4.09330.20861460.157581118257100
4.0933-5.15670.16571410.136880898230100
5.1567-58.63120.17791450.168118826399

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