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- PDB-8w08: Crystal Structure of the worst case reconstruction of the ancestr... -

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Basic information

Entry
Database: PDB / ID: 8w08
TitleCrystal Structure of the worst case reconstruction of the ancestral triosephosphate isomerase of the last opisthokont common ancestor obtained by maximum likelihood
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / Triosephosphate isomerase / ancestral sequence reconstruction
Function / homologyFLUORIDE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 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

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Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7883
Polymers58,7692
Non-polymers191
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-22 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.461, 106.831, 114.792
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-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium fluoride, 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 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Feb 4, 2019 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.88→32.52 Å / Num. obs: 43361 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.999 / Χ2: 0.98 / Net I/σ(I): 20.7
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2757 / CC1/2: 0.875 / Χ2: 0.87

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→32.52 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 1500 3.46 %
Rwork0.1931 --
obs0.1942 43361 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→32.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3717 0 1 340 4058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083826
X-RAY DIFFRACTIONf_angle_d0.9345202
X-RAY DIFFRACTIONf_dihedral_angle_d14.0121392
X-RAY DIFFRACTIONf_chiral_restr0.063601
X-RAY DIFFRACTIONf_plane_restr0.012673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.940.27461400.24553763X-RAY DIFFRACTION100
1.94-2.010.26871300.23323739X-RAY DIFFRACTION100
2.01-2.090.30541380.22633739X-RAY DIFFRACTION100
2.09-2.190.27731240.22563740X-RAY DIFFRACTION100
2.19-2.30.24081310.21443786X-RAY DIFFRACTION100
2.3-2.450.22131410.21163774X-RAY DIFFRACTION100
2.45-2.630.271350.21693773X-RAY DIFFRACTION100
2.63-2.90.21191370.21773809X-RAY DIFFRACTION100
2.9-3.320.22381370.20473826X-RAY DIFFRACTION100
3.32-4.180.20961420.17123867X-RAY DIFFRACTION100
4.18-32.520.1931450.15544045X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.19 Å / Origin y: -19.5015 Å / Origin z: 9.0496 Å
111213212223313233
T0.1803 Å2-0.0058 Å20.0085 Å2-0.1998 Å20.0567 Å2--0.1594 Å2
L0.9717 °20.4264 °20.4283 °2-1.813 °2-0.0752 °2--1.6752 °2
S0.069 Å °0.018 Å °-0.0496 Å °0.1766 Å °-0.1855 Å °-0.1085 Å °0.0781 Å °0.1412 Å °0.0848 Å °
Refinement TLS groupSelection details: all

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