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- PDB-5mvr: Crystal structure of Bacillus subtilus YdiB -

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Basic information

Entry
Database: PDB / ID: 5mvr
TitleCrystal structure of Bacillus subtilus YdiB
ComponentstRNA threonylcarbamoyladenosine biosynthesis protein TsaE
KeywordsTRANSFERASE / kinase / ADP / phosphorylation
Function / homologytRNA threonylcarbamoyl adenosine modification protein TsaE / Threonylcarbamoyl adenosine biosynthesis protein TsaE / tRNA threonylcarbamoyladenosine modification / P-loop containing nucleoside triphosphate hydrolase / ATP binding / metal ion binding / cytoplasm / ADENOSINE-5'-DIPHOSPHATE / tRNA threonylcarbamoyladenosine biosynthesis protein TsaE
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.762 Å
AuthorsJault, J.-M. / Aghajari, N.
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Expanding the Kinome World: A New Protein Kinase Family Widely Conserved in Bacteria.
Authors: Nguyen, H.A. / El Khoury, T. / Guiral, S. / Laaberki, M.H. / Candusso, M.P. / Galisson, F. / Foucher, A.E. / Kesraoui, S. / Ballut, L. / Vallet, S. / Orelle, C. / Zucchini, L. / Martin, J. / ...Authors: Nguyen, H.A. / El Khoury, T. / Guiral, S. / Laaberki, M.H. / Candusso, M.P. / Galisson, F. / Foucher, A.E. / Kesraoui, S. / Ballut, L. / Vallet, S. / Orelle, C. / Zucchini, L. / Martin, J. / Page, A. / Attieh, J. / Aghajari, N. / Grangeasse, C. / Jault, J.M.
History
DepositionJan 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: tRNA threonylcarbamoyladenosine biosynthesis protein TsaE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9466
Polymers18,3091
Non-polymers6385
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-8 kcal/mol
Surface area8030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.590, 59.820, 39.340
Angle α, β, γ (deg.)90.00, 110.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein tRNA threonylcarbamoyladenosine biosynthesis protein TsaE / t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaE


Mass: 18308.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chain break from residue 59-62 (incl.) and 85-90 (incl.) due to missing electron density. The three C-ter residues are lacking in the structure due to missing electron density. The four ...Details: Chain break from residue 59-62 (incl.) and 85-90 (incl.) due to missing electron density. The three C-ter residues are lacking in the structure due to missing electron density. The four initial N-ter residues come from the His-Tag. Mismatch is due to ADP aligning with C-ter residues
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: tsaE, ydiB, BSU05910 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O05515
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 42 % PEG600 and 200 mM Imidazole malate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07252 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2016
RadiationMonochromator: liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07252 Å / Relative weight: 1
ReflectionResolution: 1.76→43.84 Å / Num. obs: 14655 / % possible obs: 98.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 16.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HTW

1htw


Resolution: 1.762→43.835 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 708 4.83 %
Rwork0.1802 --
obs0.1816 14651 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.762→43.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1161 0 40 57 1258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081235
X-RAY DIFFRACTIONf_angle_d1.2271669
X-RAY DIFFRACTIONf_dihedral_angle_d19.29731
X-RAY DIFFRACTIONf_chiral_restr0.062184
X-RAY DIFFRACTIONf_plane_restr0.006210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7617-1.89770.31071470.27162674X-RAY DIFFRACTION95
1.8977-2.08870.23541410.20192787X-RAY DIFFRACTION99
2.0887-2.39090.21591280.18132820X-RAY DIFFRACTION99
2.3909-3.01220.22291490.19662813X-RAY DIFFRACTION100
3.0122-43.84820.19011430.16382849X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -0.1199 Å / Origin y: 3.1225 Å / Origin z: 49.5559 Å
111213212223313233
T0.2082 Å20.0166 Å2-0.0001 Å2-0.2395 Å2-0.03 Å2--0.2398 Å2
L4.3913 °20.297 °2-0.4006 °2-3.5861 °20.2898 °2--4.2506 °2
S0.0019 Å °0.2468 Å °-0.0146 Å °-0.1373 Å °-0.2538 Å °-0.0135 Å °0.0518 Å °-0.3902 Å °0.1993 Å °
Refinement TLS groupSelection details: all

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