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- PDB-7mxk: Crystal structure of the S/T protein kinase PknG from Corynebacte... -

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Basic information

Entry
Database: PDB / ID: 7mxk
TitleCrystal structure of the S/T protein kinase PknG from Corynebacterium glutamicum (residues 130-433) in complex with AMP-PNP, isoform 2
ComponentsSerine/threonine protein kinases
KeywordsTRANSFERASE / metabolic control / glutamate metabolism / bacterial protein kinase / tetratricopeptide repeats
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding / metal ion binding
Similarity search - Function
Protein kinase G, tetratricopeptide repeat containing domain / Protein kinase G tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. ...Protein kinase G, tetratricopeptide repeat containing domain / Protein kinase G tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
MAGNESIUM-5'-ADENYLY-IMIDO-TRIPHOSPHATE / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsLisa, M.N. / Alzari, P.M.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-09-BLAN-0400 France
CitationJournal: Mbio / Year: 2021
Title: A Tetratricopeptide Repeat Scaffold Couples Signal Detection to OdhI Phosphorylation in Metabolic Control by the Protein Kinase PknG.
Authors: Lisa, M.N. / Sogues, A. / Barilone, N. / Baumgart, M. / Gil, M. / Grana, M. / Duran, R. / Biondi, R.M. / Bellinzoni, M. / Bott, M. / Alzari, P.M.
History
DepositionMay 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 10, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine protein kinases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8263
Polymers33,2721
Non-polymers5542
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.807, 54.594, 146.492
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Serine/threonine protein kinases


Mass: 33272.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: Cgl2751 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NM29
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MAP / MAGNESIUM-5'-ADENYLY-IMIDO-TRIPHOSPHATE


Mass: 529.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16MgN6O12P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 100 mM Tris-HCl, 27-30% w/v PEG 4 k, 200 mM MgCl2, pH 8.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.99→48.83 Å / Num. obs: 21235 / % possible obs: 98.4 % / Redundancy: 6 % / Biso Wilson estimate: 29.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.029 / Rrim(I) all: 0.073 / Net I/σ(I): 17.1
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.654 / Num. unique obs: 1207 / CC1/2: 0.751 / Rpim(I) all: 0.306 / Rrim(I) all: 0.725 / % possible all: 84.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7MXB

7mxb


Resolution: 1.99→43.77 Å / SU ML: 0.222 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3222
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237 1063 5.02 %
Rwork0.2088 20120 -
obs0.2102 21183 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.13 Å2
Refinement stepCycle: LAST / Resolution: 1.99→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 33 157 2445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00292337
X-RAY DIFFRACTIONf_angle_d0.61323183
X-RAY DIFFRACTIONf_chiral_restr0.0486359
X-RAY DIFFRACTIONf_plane_restr0.0051412
X-RAY DIFFRACTIONf_dihedral_angle_d14.4908881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.080.32961230.29982166X-RAY DIFFRACTION87.13
2.08-2.190.2661440.26862475X-RAY DIFFRACTION98.87
2.19-2.330.2891310.24512515X-RAY DIFFRACTION99.7
2.33-2.510.29961210.24292546X-RAY DIFFRACTION99.59
2.51-2.760.29121420.23282527X-RAY DIFFRACTION99.89
2.76-3.160.27741220.22492577X-RAY DIFFRACTION99.78
3.16-3.980.2281280.19012588X-RAY DIFFRACTION99.85
3.98-43.770.17021520.16862726X-RAY DIFFRACTION99.79
Refinement TLS params.Method: refined / Origin x: -0.113720250801 Å / Origin y: 17.565592884 Å / Origin z: -18.6506305899 Å
111213212223313233
T0.209507781257 Å20.00958499352637 Å20.0488829267095 Å2-0.27981046034 Å20.0807125523547 Å2--0.204330018334 Å2
L1.33936941846 °2-1.30200038833 °2-0.56529736293 °2-5.68714081356 °21.64867626222 °2--3.54245112021 °2
S-0.318495101762 Å °-0.35055177634 Å °-0.232347571691 Å °0.741392192608 Å °0.309396924 Å °0.43504957546 Å °-0.104200310369 Å °0.315164328652 Å °0.0124300699966 Å °
Refinement TLS groupSelection details: all

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