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- PDB-8v2x: Crystal Structure of the reconstruction of the worst case of the ... -

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Basic information

Entry
Database: PDB / ID: 8v2x
TitleCrystal Structure of the reconstruction of the worst case of the ancestral triosephosphate isomerase 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: 1.43 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 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


Theoretical massNumber of molelcules
Total (without water)29,4221
Polymers29,4221
Non-polymers00
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.205, 59.535, 114.789
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: 29421.518 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350 , 0.2 M NaF

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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: Nov 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.43→46.2 Å / Num. obs: 58029 / % possible obs: 98 % / Redundancy: 5.4 % / CC1/2: 0.997 / Χ2: 0.71 / Net I/σ(I): 23.9
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2619 / CC1/2: 0.86 / Χ2: 0.42 / % possible all: 90.6

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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: 1.43→36.5 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 16.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1793 2917 5.03 %
Rwork0.1784 --
obs0.1784 58029 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.43→36.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 0 330 2232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082096
X-RAY DIFFRACTIONf_angle_d1.0392857
X-RAY DIFFRACTIONf_dihedral_angle_d13.63798
X-RAY DIFFRACTIONf_chiral_restr0.093320
X-RAY DIFFRACTIONf_plane_restr0.012379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.21561310.23122377X-RAY DIFFRACTION90
1.45-1.480.23911320.21932477X-RAY DIFFRACTION94
1.48-1.510.20311160.21992496X-RAY DIFFRACTION94
1.51-1.530.23191440.21772508X-RAY DIFFRACTION95
1.53-1.570.21841380.20042529X-RAY DIFFRACTION95
1.57-1.60.21461280.1982554X-RAY DIFFRACTION96
1.6-1.640.18551420.19622573X-RAY DIFFRACTION97
1.64-1.680.22231190.19682584X-RAY DIFFRACTION97
1.68-1.720.2141480.19242600X-RAY DIFFRACTION98
1.72-1.770.19811410.19692612X-RAY DIFFRACTION98
1.77-1.830.19421460.20672621X-RAY DIFFRACTION99
1.83-1.90.20451440.19542641X-RAY DIFFRACTION99
1.9-1.970.1881250.17872674X-RAY DIFFRACTION100
1.97-2.060.19621380.18412685X-RAY DIFFRACTION100
2.06-2.170.19881370.18172690X-RAY DIFFRACTION100
2.17-2.310.18151420.17312700X-RAY DIFFRACTION100
2.31-2.490.17361520.1752684X-RAY DIFFRACTION100
2.49-2.740.15961650.17642697X-RAY DIFFRACTION100
2.74-3.130.17681500.16992739X-RAY DIFFRACTION100
3.13-3.940.1511320.1552764X-RAY DIFFRACTION100
3.94-36.50.13631470.15272907X-RAY DIFFRACTION100

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