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- PDB-8v0a: Crystal Structure of the worst case of the reconstruction of the ... -

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Basic information

Entry
Database: PDB / ID: 8v0a
TitleCrystal Structure of the worst case of the reconstruction of the ancestral triosephosphate isomerase of the last opisthokont common ancestor obtained by maximum likelihood with PGH
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / Triose phosphate isomerase / Ancestral sequence reconstruction
Function / homologyPHOSPHOGLYCOLOHYDROXAMIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 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
DepositionNov 17, 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
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9403
Polymers58,7692
Non-polymers1711
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-28 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.716, 106.379, 114.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Triosephosphate isomerase


Mass: 29384.361 Da / Num. of mol.: 2
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-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 / Details: 0.2 M Ammonium citrate dibasic, 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 27, 2018 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.046→39.183 Å / Num. obs: 32427 / % possible obs: 98.39 % / Redundancy: 7.1 % / CC1/2: 0.897 / Χ2: 6.046 / Net I/σ(I): 17.46
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1630 / CC1/2: 0.593 / % possible all: 98.3

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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: 2.05→39.18 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2429 1643 5.07 %
Rwork0.1968 --
obs0.1991 32427 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 10 314 4133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093915
X-RAY DIFFRACTIONf_angle_d1.0625313
X-RAY DIFFRACTIONf_dihedral_angle_d15.3241452
X-RAY DIFFRACTIONf_chiral_restr0.07607
X-RAY DIFFRACTIONf_plane_restr0.009687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.110.35651240.29642430X-RAY DIFFRACTION95
2.11-2.170.26841510.25592530X-RAY DIFFRACTION99
2.17-2.250.29211550.24262488X-RAY DIFFRACTION99
2.25-2.340.27871270.22932560X-RAY DIFFRACTION99
2.34-2.450.2961310.22852548X-RAY DIFFRACTION99
2.45-2.580.27891510.23872511X-RAY DIFFRACTION98
2.58-2.740.28531150.21912570X-RAY DIFFRACTION98
2.74-2.950.25621470.2232547X-RAY DIFFRACTION98
2.95-3.250.22731250.19822581X-RAY DIFFRACTION99
3.25-3.720.22881340.1712598X-RAY DIFFRACTION99
3.72-4.680.1731330.14432652X-RAY DIFFRACTION99
4.68-39.180.21461500.16182769X-RAY DIFFRACTION99

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