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

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Basic information

Entry
Database: PDB / ID: 7mxj
TitleCrystal structure of the S/T protein kinase PknG from Corynebacterium glutamicum (residues 130-433) in complex with AMP-PNP, isoform 1
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: 1.92 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
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.616, 55.936, 123.945
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.: 237 / 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: 1.96 Å3/Da / Density % sol: 37.23 %
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: 1.92→41.52 Å / Num. obs: 20752 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 28.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.031 / Rrim(I) all: 0.077 / Net I/σ(I): 13.6
Reflection shellResolution: 1.92→1.97 Å / Rmerge(I) obs: 0.746 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1378 / CC1/2: 0.805 / Rpim(I) all: 0.343 / Rrim(I) all: 0.823

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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: 1.92→41.52 Å / SU ML: 0.2763 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7487
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2246 1001 4.84 %
Rwork0.1989 19700 -
obs0.2001 20701 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.84 Å2
Refinement stepCycle: LAST / Resolution: 1.92→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2190 0 33 237 2460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342270
X-RAY DIFFRACTIONf_angle_d0.68643095
X-RAY DIFFRACTIONf_chiral_restr0.0496352
X-RAY DIFFRACTIONf_plane_restr0.0048400
X-RAY DIFFRACTIONf_dihedral_angle_d13.6821845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-2.020.36651470.29462739X-RAY DIFFRACTION99.9
2.02-2.150.29191410.25052759X-RAY DIFFRACTION99.9
2.15-2.310.26861300.21162797X-RAY DIFFRACTION99.93
2.31-2.550.23921530.19852775X-RAY DIFFRACTION99.97
2.55-2.910.23891340.1972821X-RAY DIFFRACTION99.97
2.92-3.670.19061490.18282821X-RAY DIFFRACTION99.9
3.67-41.520.20211470.18542988X-RAY DIFFRACTION99.65
Refinement TLS params.Method: refined / Origin x: -2.06013173313 Å / Origin y: 13.759249666 Å / Origin z: -16.4702413149 Å
111213212223313233
T0.18398076869 Å2-0.0236739698674 Å2-0.00024236817476 Å2-0.197617809618 Å20.0122562705542 Å2--0.182809142164 Å2
L0.821045421139 °2-0.308003568322 °20.0980077142508 °2-1.70445310197 °20.406835969622 °2--1.27179596665 °2
S-0.0371126263206 Å °-0.0109617687566 Å °0.0517276006366 Å °0.187041564026 Å °0.0483922980617 Å °0.0156345531162 Å °-0.0729024984163 Å °0.0650711153125 Å °-0.0147969015051 Å °
Refinement TLS groupSelection details: all

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