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- PDB-5np9: Crystal structure of Bacillus subtilis YdiB in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 5np9
TitleCrystal structure of Bacillus subtilis YdiB in complex with ADP
ComponentstRNA threonylcarbamoyladenosine biosynthesis protein TsaE
KeywordsTRANSFERASE / Kinase / ADP / phosphorylastion
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: 2 Å
AuthorsBallut, L. / 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
DepositionApr 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 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)18,3793
Polymers17,9271
Non-polymers4522
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-15 kcal/mol
Surface area7560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.030, 111.770, 35.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 17927.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: construction different fron that used for pdb entry 5MVR There is a flexible region from residue 87-89 and no electron density is visible for residues 87 and 88. As concnerns residue 89, ...Details: construction different fron that used for pdb entry 5MVR There is a flexible region from residue 87-89 and no electron density is visible for residues 87 and 88. As concnerns residue 89, there is no density for the side-chain. Hereafter, the sequence is complete until residue 154 (incl.) and from then on there is no more electron density.
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: isolated from a natural source / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 4000, 200 mM MgCl2 and 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2017
RadiationMonochromator: Liquid nitrogen cooled silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.05→34.06 Å / Num. obs: 10574 / % possible obs: 97.1 % / Redundancy: 3.7 % / Net I/σ(I): 8.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MVR

5mvr


Resolution: 2→34.059 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2278 573 5.01 %
Rwork0.1742 --
obs0.1768 11439 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→34.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1206 0 28 86 1320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061257
X-RAY DIFFRACTIONf_angle_d0.9341703
X-RAY DIFFRACTIONf_dihedral_angle_d12.504745
X-RAY DIFFRACTIONf_chiral_restr0.054189
X-RAY DIFFRACTIONf_plane_restr0.004215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.20130.30381410.23392669X-RAY DIFFRACTION98
2.2013-2.51970.251420.19522704X-RAY DIFFRACTION98
2.5197-3.17420.23671440.19012724X-RAY DIFFRACTION98
3.1742-34.0640.20631460.15252769X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 25.3866 Å / Origin y: 16.5229 Å / Origin z: -3.4841 Å
111213212223313233
T0.2029 Å20.0188 Å20.0451 Å2-0.2003 Å20.0208 Å2--0.195 Å2
L1.323 °2-0.5086 °20.2565 °2-3.722 °2-0.1383 °2--3.9269 °2
S-0.0187 Å °0.0028 Å °-0.1212 Å °-0.2263 Å °-0.0552 Å °-0.1675 Å °0.4074 Å °0.0744 Å °0.0294 Å °
Refinement TLS groupSelection details: all

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