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- PDB-8v09: Crystal Structure of the reconstruction of the ancestral trioseph... -

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Basic information

Entry
Database: PDB / ID: 8v09
TitleCrystal Structure of the reconstruction of the ancestral triosephosphate isomerase of the last opisthokont common ancestor obtained by bayesian inference with PGH
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / Triose phosphate isomerase / Ancestral sequence reconstruction
Function / homologyACETIC ACID / FORMIC ACID / PHOSPHOGLYCOLOHYDROXAMIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsPerez-Nino, J.A. / Rodriguez-Romero, A. / Guerra-Borrego, Y. / Fernandez-Velasco, D.A.
Funding support Mexico, 2items
OrganizationGrant numberCountry
Other governmentIV200322 Mexico
Other governmentIN210519 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8598
Polymers29,4071
Non-polymers4527
Water6,053336
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.647, 59.467, 114.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 1 molecules A

#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-28(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD / References: triose-phosphate isomerase

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Non-polymers , 5 types, 343 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6NO6P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 4% v/v Tacsimate, 12% 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: Feb 1, 2018 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.61→34.95 Å / Num. obs: 41912 / % possible obs: 99.74 % / Redundancy: 5.2 % / CC1/2: 0.942 / Χ2: 0.79 / Net I/σ(I): 10.6
Reflection shellResolution: 1.61→1.65 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2004 / CC1/2: 0.648 / Χ2: 0.43 / % possible all: 99.9

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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: 1.61→34.95 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1734 2067 4.93 %
Rwork0.1652 --
obs0.1656 41912 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→34.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 28 336 2259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112041
X-RAY DIFFRACTIONf_angle_d1.2962763
X-RAY DIFFRACTIONf_dihedral_angle_d14.193762
X-RAY DIFFRACTIONf_chiral_restr0.088304
X-RAY DIFFRACTIONf_plane_restr0.008364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.650.2151360.20682602X-RAY DIFFRACTION100
1.65-1.690.20941240.19272595X-RAY DIFFRACTION100
1.69-1.730.21011380.18482642X-RAY DIFFRACTION100
1.73-1.790.20451240.18062644X-RAY DIFFRACTION100
1.79-1.840.19531350.18262644X-RAY DIFFRACTION100
1.84-1.910.18371360.17572604X-RAY DIFFRACTION100
1.91-1.990.18651610.16282633X-RAY DIFFRACTION100
1.99-2.080.22791340.21242561X-RAY DIFFRACTION98
2.08-2.180.15861330.15622661X-RAY DIFFRACTION100
2.19-2.320.1671350.15252651X-RAY DIFFRACTION100
2.32-2.50.15581280.16182677X-RAY DIFFRACTION100
2.5-2.750.17731640.15142660X-RAY DIFFRACTION100
2.75-3.150.1581270.1572710X-RAY DIFFRACTION100
3.15-3.970.15811370.1482713X-RAY DIFFRACTION100
3.97-34.950.14091550.15192848X-RAY DIFFRACTION100

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