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- PDB-8v2w: Crystal Structure of the ancestral triosephosphate isomerase reco... -

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Basic information

Entry
Database: PDB / ID: 8v2w
TitleCrystal Structure of the ancestral triosephosphate isomerase reconstruction of the last opisthokont common ancestor obtained by Bayesian inference
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / Triose phosphate isomerase / Ancestral sequence reconstruction
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsPerez-Nino, J.A. / Rodriguez-Romero, A. / Guerra, 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
DepositionNov 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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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)29,4992
Polymers29,4071
Non-polymers921
Water5,242291
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.525, 47.579, 64.308
Angle α, β, γ (deg.)90.00, 126.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Triosephosphate isomerase


Mass: 29406.572 Da / Num. of mol.: 1
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 1.97 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M BICINE pH 8.5, 15 % w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Aug 30, 2018 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.38→31.912 Å / Num. obs: 46451 / % possible obs: 98.53 % / Redundancy: 3.2 % / CC1/2: 0.91 / Rmerge(I) obs: 0.073 / Χ2: 2.242 / Net I/σ(I): 27.3
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2 / Num. unique obs: 2219 / CC1/2: 0.59 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→31.91 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1699 2333 5.02 %
Rwork0.1605 --
obs0.161 46451 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.38→31.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 6 291 2192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122120
X-RAY DIFFRACTIONf_angle_d1.2672885
X-RAY DIFFRACTIONf_dihedral_angle_d13.937817
X-RAY DIFFRACTIONf_chiral_restr0.09316
X-RAY DIFFRACTIONf_plane_restr0.008382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.410.29761160.27192167X-RAY DIFFRACTION83
1.41-1.440.26291210.25182569X-RAY DIFFRACTION98
1.44-1.470.24981290.22662579X-RAY DIFFRACTION98
1.47-1.510.24831340.20372590X-RAY DIFFRACTION99
1.51-1.550.23261490.19312577X-RAY DIFFRACTION99
1.55-1.60.20131330.18432611X-RAY DIFFRACTION99
1.6-1.650.22241440.17962631X-RAY DIFFRACTION99
1.65-1.710.1991240.17432622X-RAY DIFFRACTION100
1.71-1.770.21641510.16372606X-RAY DIFFRACTION100
1.77-1.850.16991350.16322627X-RAY DIFFRACTION100
1.85-1.950.17631170.15172642X-RAY DIFFRACTION100
1.95-2.070.16241550.15632619X-RAY DIFFRACTION100
2.07-2.230.17821420.15342617X-RAY DIFFRACTION100
2.23-2.460.16861470.15262635X-RAY DIFFRACTION100
2.46-2.810.15761460.15532636X-RAY DIFFRACTION100
2.82-3.550.15261470.14732671X-RAY DIFFRACTION100
3.55-31.910.12771430.14172719X-RAY DIFFRACTION100

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