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- PDB-8w06: Crystal Structure of the reconstruction of the ancestral trioseph... -

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Basic information

Entry
Database: PDB / ID: 8w06
TitleCrystal Structure 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 / homologyACETATE ION / ACETIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHOGLYCOLOHYDROXAMIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 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
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
C: Triosephosphate isomerase
D: Triosephosphate isomerase
E: Triosephosphate isomerase
F: Triosephosphate isomerase
G: Triosephosphate isomerase
H: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,76724
Polymers236,7978
Non-polymers1,97016
Water22,8611269
1
C: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7506
Polymers59,1992
Non-polymers5514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area4130 Å2
ΔGint-38 kcal/mol
Surface area19210 Å2
MethodPISA
2
B: Triosephosphate isomerase
D: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6867
Polymers59,1992
Non-polymers4875
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-46 kcal/mol
Surface area19090 Å2
MethodPISA
3
E: Triosephosphate isomerase
F: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6836
Polymers59,1992
Non-polymers4844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-34 kcal/mol
Surface area19000 Å2
MethodPISA
4
G: Triosephosphate isomerase
H: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6475
Polymers59,1992
Non-polymers4483
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-30 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.642, 83.222, 127.865
Angle α, β, γ (deg.)90.00, 103.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Triosephosphate isomerase


Mass: 29599.588 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Ancestral sequence reconstruction of the opisthokont common ancestor
Source: (gene. exp.) synthetic construct (others) / Plasmid: plasmid / Details (production host): pET-28T(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD / References: triose-phosphate isomerase

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Non-polymers , 9 types, 1285 molecules

#2: Chemical
ChemComp-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C2H6NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1269 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium acetate tetrahydrate, 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 13, 2018 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.06→41.45 Å / Num. obs: 140270 / % possible obs: 99.53 % / Redundancy: 6.2 % / CC1/2: 0.994 / Χ2: 0.86 / Net I/σ(I): 7.6
Reflection shellResolution: 2.06→2.08 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2 / Num. unique obs: 6620 / CC1/2: 0.535 / Χ2: 0.68 / % possible all: 95.4

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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: 2.06→41.45 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 7108 5.07 %
Rwork0.1949 --
obs0.1969 140270 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15353 0 118 1269 16740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915878
X-RAY DIFFRACTIONf_angle_d0.94121504
X-RAY DIFFRACTIONf_dihedral_angle_d16.3595875
X-RAY DIFFRACTIONf_chiral_restr0.062434
X-RAY DIFFRACTIONf_plane_restr0.0082790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.080.31042160.2644264X-RAY DIFFRACTION96
2.08-2.110.28972330.24514393X-RAY DIFFRACTION98
2.11-2.130.30732280.24514402X-RAY DIFFRACTION99
2.13-2.160.29452250.23434377X-RAY DIFFRACTION100
2.16-2.190.27862050.23334525X-RAY DIFFRACTION100
2.19-2.220.27662480.23574320X-RAY DIFFRACTION100
2.22-2.250.30172450.23684477X-RAY DIFFRACTION100
2.25-2.280.29492320.23374413X-RAY DIFFRACTION100
2.28-2.320.30562370.23314432X-RAY DIFFRACTION100
2.32-2.360.28362400.23154403X-RAY DIFFRACTION100
2.36-2.40.29512320.22224412X-RAY DIFFRACTION100
2.4-2.440.2622420.21924479X-RAY DIFFRACTION100
2.44-2.490.28582200.22624363X-RAY DIFFRACTION100
2.49-2.540.27072420.22584493X-RAY DIFFRACTION100
2.54-2.60.30582370.21974421X-RAY DIFFRACTION100
2.6-2.660.23782140.20734446X-RAY DIFFRACTION100
2.66-2.720.2572170.22264481X-RAY DIFFRACTION100
2.72-2.80.29632250.24014450X-RAY DIFFRACTION100
2.8-2.880.28532340.22524454X-RAY DIFFRACTION100
2.88-2.970.24682440.2154436X-RAY DIFFRACTION100
2.97-3.080.25562580.21694406X-RAY DIFFRACTION100
3.08-3.20.26062510.2184455X-RAY DIFFRACTION100
3.2-3.350.25892370.21274460X-RAY DIFFRACTION100
3.35-3.520.24232300.18974442X-RAY DIFFRACTION100
3.52-3.740.20132630.17824474X-RAY DIFFRACTION100
3.74-4.030.19622360.16324450X-RAY DIFFRACTION99
4.03-4.440.16552390.1524448X-RAY DIFFRACTION100
4.44-5.080.19092560.14564507X-RAY DIFFRACTION100
5.08-6.390.20662680.17464504X-RAY DIFFRACTION100
6.39-41.450.17562540.15094575X-RAY DIFFRACTION99

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