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- PDB-8w05: Crystal Structure of the reconstruction of the ancestral trioseph... -

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Basic information

Entry
Database: PDB / ID: 8w05
TitleCrystal Structure of the reconstruction of the ancestral triosephosphate isomerase of the last opisthokont common ancestor obtained by maximum likelihood
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / Triose phosphate isomerase / Ancestral sequence reconstruction
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsPerez-Nino, J.A. / Rodriguez-Romero, A. / Guerra-Borrego, Y. / Fernandez-Velasco, D.A.
Funding support Mexico, 2items
OrganizationGrant numberCountry
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IV200322 Mexico
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IN210519 Mexico
CitationJournal: Protein Sci. / Year: 2024
Title: Stable monomers in the ancestral sequence reconstruction of the last opisthokont common ancestor of dimeric triosephosphate isomerase.
Authors: Perez-Nino, J.A. / Guerra, Y. / Diaz-Salazar, A.J. / Costas, M. / Rodriguez-Romero, A. / Fernandez-Velasco, D.A.
History
DepositionFeb 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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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
E: Triosephosphate isomerase
F: Triosephosphate isomerase
G: Triosephosphate isomerase
H: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)236,7978
Polymers236,7978
Non-polymers00
Water20,3751131
1
A: Triosephosphate isomerase

F: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)59,1992
Polymers59,1992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area3220 Å2
ΔGint-27 kcal/mol
Surface area18910 Å2
MethodPISA
2
B: Triosephosphate isomerase

E: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)59,1992
Polymers59,1992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-x,y-1/2,-z-11
Buried area3190 Å2
ΔGint-27 kcal/mol
Surface area19400 Å2
MethodPISA
3
C: Triosephosphate isomerase
D: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)59,1992
Polymers59,1992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-27 kcal/mol
Surface area18940 Å2
MethodPISA
4
G: Triosephosphate isomerase

H: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)59,1992
Polymers59,1992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Buried area3190 Å2
ΔGint-27 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.416, 83.597, 126.016
Angle α, β, γ (deg.)90.00, 105.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Triosephosphate isomerase


Mass: 29599.588 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Ancestral sequence reconstruction of the opisthokont common ancestor
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-28T(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD / References: triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1131 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.2 M Sodium malonate pH 5.0, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Sep 6, 2018 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.16→43.8 Å / Num. obs: 113623 / % possible obs: 98.22 % / Redundancy: 4.4 % / CC1/2: 0.905 / Net I/av σ(I): 15.5 / Net I/σ(I): 15.6
Reflection shellResolution: 2.165→2.2 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.05 / Num. unique obs: 5644 / CC1/2: 0.692

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→43.8 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2399 5621 4.95 %
Rwork0.1898 --
obs0.1923 113623 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15279 0 0 1131 16410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815588
X-RAY DIFFRACTIONf_angle_d0.93821120
X-RAY DIFFRACTIONf_dihedral_angle_d15.1425750
X-RAY DIFFRACTIONf_chiral_restr0.062413
X-RAY DIFFRACTIONf_plane_restr0.0092743
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.190.35971610.27823229X-RAY DIFFRACTION88
2.19-2.210.32791930.27663589X-RAY DIFFRACTION99
2.21-2.240.31371790.27633593X-RAY DIFFRACTION99
2.24-2.270.35851760.26293623X-RAY DIFFRACTION99
2.27-2.30.31951820.24683627X-RAY DIFFRACTION99
2.3-2.330.33141630.25583640X-RAY DIFFRACTION99
2.33-2.370.28722010.24663593X-RAY DIFFRACTION99
2.37-2.40.30351790.23183649X-RAY DIFFRACTION99
2.4-2.440.30711680.24193602X-RAY DIFFRACTION99
2.44-2.480.37582080.24973533X-RAY DIFFRACTION98
2.48-2.520.31771800.2443683X-RAY DIFFRACTION99
2.52-2.570.29811830.24023556X-RAY DIFFRACTION98
2.57-2.620.28062040.22363579X-RAY DIFFRACTION98
2.62-2.670.29511980.22513595X-RAY DIFFRACTION99
2.67-2.730.34912100.24833565X-RAY DIFFRACTION98
2.73-2.790.29482000.24023604X-RAY DIFFRACTION98
2.79-2.860.31700.21573577X-RAY DIFFRACTION98
2.86-2.940.24381760.20353580X-RAY DIFFRACTION98
2.94-3.020.25351970.21553604X-RAY DIFFRACTION98
3.02-3.120.28751820.21063567X-RAY DIFFRACTION98
3.12-3.230.28781820.2093636X-RAY DIFFRACTION98
3.23-3.360.28561800.20263600X-RAY DIFFRACTION98
3.36-3.520.20781910.18123556X-RAY DIFFRACTION97
3.52-3.70.21661850.16363624X-RAY DIFFRACTION99
3.7-3.930.1822050.1533634X-RAY DIFFRACTION99
3.93-4.240.1711850.14623552X-RAY DIFFRACTION97
4.24-4.660.18191920.12643671X-RAY DIFFRACTION99
4.66-5.340.17612090.13443633X-RAY DIFFRACTION99
5.34-6.720.16441920.163706X-RAY DIFFRACTION100
6.72-43.80.16841900.14253802X-RAY DIFFRACTION99

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