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- PDB-6g4j: Structure of the protein kinase YabT from Bacillus subtilis in co... -

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Basic information

Entry
Database: PDB / ID: 6g4j
TitleStructure of the protein kinase YabT from Bacillus subtilis in complex with an alphaREP crystallization helper
Components
  • Probable serine/threonine-protein kinase YabT
  • alphaREP bE8
KeywordsTRANSFERASE / Bacterial Hanks-type protein kinase / complex with an artificial binder / SIGNALING PROTEIN
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Probable serine/threonine-protein kinase YabT
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.599 Å
AuthorsNessler, S. / Cavagnino, A. / Rabefiraisana, J.L.
CitationJournal: Front Microbiol / Year: 2018
Title: Structural Analysis of the Hanks-Type Protein Kinase YabT FromBacillus subtilisProvides New Insights in its DNA-Dependent Activation.
Authors: Shi, L. / Cavagnino, A. / Rabefiraisana, J.L. / Lazar, N. / Li de la Sierra-Gallay, I. / Ochsenbein, F. / Valerio-Lepiniec, M. / Urvoas, A. / Minard, P. / Mijakovic, I. / Nessler, S.
History
DepositionMar 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Probable serine/threonine-protein kinase YabT
B: alphaREP bE8


Theoretical massNumber of molelcules
Total (without water)50,8882
Polymers50,8882
Non-polymers00
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The bE8 alphaREP binder makes tight and specific contacts with YabT
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-7 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.690, 122.870, 50.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Probable serine/threonine-protein kinase YabT


Mass: 35023.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The C-terminal transmembrane helix of YabT (residues 316-338) has been deleted. The juxtamembrane region (residues 274-315) is disordered.
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: yabT, BSU00660 / Production host: Escherichia coli BL21(DE3) / Variant (production host): Rosetta
References: UniProt: P37562, non-specific serine/threonine protein kinase
#2: Protein alphaREP bE8


Mass: 15864.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The N-terminal His-tag and the C-terminal linker are disordered.
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5 / Details: PEG 8000, Hepes,

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.599→50 Å / Num. all: 203500 / Num. obs: 56285 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rrim(I) all: 0.053 / Net I/σ(I): 14.11
Reflection shellResolution: 1.599→1.7 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.28 / Num. unique obs: 8958 / % possible all: 98.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.66 Å40.51 Å
Translation5.66 Å40.51 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.599→40.513 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.18
RfactorNum. reflection% reflection
Rfree0.2169 2814 5 %
Rwork0.1889 --
obs0.1903 56281 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.28 Å2 / Biso mean: 32.7074 Å2 / Biso min: 15.78 Å2
Refinement stepCycle: final / Resolution: 1.599→40.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3058 0 0 227 3285
Biso mean---36.53 -
Num. residues----395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063140
X-RAY DIFFRACTIONf_angle_d1.0174247
X-RAY DIFFRACTIONf_chiral_restr0.037474
X-RAY DIFFRACTIONf_plane_restr0.005545
X-RAY DIFFRACTIONf_dihedral_angle_d11.9161190
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5988-1.62640.31441370.28652590272797
1.6264-1.6560.30261380.283226282766100
1.656-1.68780.31400.274826542794100
1.6878-1.72230.30131380.264626222760100
1.7223-1.75970.29031400.258626632803100
1.7597-1.80070.25631390.234126472786100
1.8007-1.84570.2621400.227226502790100
1.8457-1.89560.26461390.212726502789100
1.8956-1.95140.25751390.21982646278599
1.9514-2.01440.24341410.203126772818100
2.0144-2.08630.20751390.197926402779100
2.0863-2.16990.23751410.193126702811100
2.1699-2.26860.21031380.19052653279199
2.2686-2.38820.22391410.19226692810100
2.3882-2.53780.24151420.1952703284599
2.5378-2.73370.21521420.195626882830100
2.7337-3.00880.22921420.196927032845100
3.0088-3.44390.23761420.18792709285199
3.4439-4.33820.20211440.16092726287099
4.3382-40.52570.15351520.15962879303199

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