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- PDB-6nee: Crystal structure of a reconstructed ancestor of Triosephosphate ... -

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Basic information

Entry
Database: PDB / ID: 6nee
TitleCrystal structure of a reconstructed ancestor of Triosephosphate isomerase from eukaryotes
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / Glycolisis / TIM Barrel / Ancestral sequence reconstruction
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / PHOSPHOGLYCOLOHYDROXAMIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRodriguez-Romero, A. / Schulte-Sasse, M. / Fernandez-Velasco, D.A.
CitationJournal: FEBS J. / Year: 2019
Title: Structural, thermodynamic and catalytic characterization of an ancestral triosephosphate isomerase reveal early evolutionary coupling between monomer association and function.
Authors: Schulte-Sasse, M. / Pardo-Avila, F. / Pulido-Mayoral, N.O. / Vazquez-Lobo, A. / Costas, M. / Garcia-Hernandez, E. / Rodriguez-Romero, A. / Fernandez-Velasco, D.A.
History
DepositionDec 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4194
Polymers55,0772
Non-polymers3422
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-38 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.020, 48.772, 71.205
Angle α, β, γ (deg.)91.28, 100.14, 118.65
Int Tables number1
Space group name H-MP1

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE /


Mass: 27538.686 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-28 b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: triose-phosphate isomerase
#2: Chemical ChemComp-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPS pH 7.5, 20% PEG 8000. Protein concentration 6 mg/mL in 10 mM Triethanolamine pH 7.6, 1 mM EDTA, 1 mM DTT, 50 mM NaCl, 10 mM PGH

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Data collection

DiffractionMean temperature: 103 K / Ambient temp details: oxford cryosystem / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 29, 2016 / Details: Mirror
RadiationMonochromator: Graphite monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→42.472 Å / Num. obs: 37060 / % possible obs: 95 % / Redundancy: 3.9 % / Biso Wilson estimate: 22.52 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Net I/σ(I): 12.3
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 3 / Num. unique obs: 2648 / % possible all: 91.4

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Processing

Software
NameVersionClassification
PHENIX(dev_3290: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I9E

2i9e


Resolution: 1.9→38.423 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2017 1871 5.05 %
Rwork0.1625 --
obs0.1646 37057 94.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→38.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3817 0 20 427 4264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013934
X-RAY DIFFRACTIONf_angle_d0.965343
X-RAY DIFFRACTIONf_dihedral_angle_d8.233286
X-RAY DIFFRACTIONf_chiral_restr0.06613
X-RAY DIFFRACTIONf_plane_restr0.007689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95140.27761500.21592643X-RAY DIFFRACTION91
1.9514-2.00880.26011170.20982600X-RAY DIFFRACTION92
2.0088-2.07360.27711230.22643X-RAY DIFFRACTION92
2.0736-2.14780.23351370.18182703X-RAY DIFFRACTION93
2.1478-2.23370.24711460.1732657X-RAY DIFFRACTION93
2.2337-2.33540.22951360.17112647X-RAY DIFFRACTION94
2.3354-2.45850.20711510.16942704X-RAY DIFFRACTION95
2.4585-2.61250.23291430.17512735X-RAY DIFFRACTION95
2.6125-2.81420.2541360.18172744X-RAY DIFFRACTION96
2.8142-3.09720.25681700.17262737X-RAY DIFFRACTION96
3.0972-3.54510.18061270.15642794X-RAY DIFFRACTION97
3.5451-4.46540.15741810.13042770X-RAY DIFFRACTION98
4.4654-38.43050.14391540.14292809X-RAY DIFFRACTION99

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