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

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Basic information

Entry
Database: PDB / ID: 7mxb
TitleCrystal structure of the S/T protein kinase PknG from Corynebacterium glutamicum in complex with AMP-PNP
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 / 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 ...Protein kinase G, tetratricopeptide repeat containing domain / Protein kinase G tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / 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 / Orthogonal Bundle / Mainly Alpha
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: 2.2 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 18, 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
B: Serine/threonine protein kinases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,5918
Polymers155,4352
Non-polymers1,1566
Water16,394910
1
A: Serine/threonine protein kinases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2964
Polymers77,7181
Non-polymers5783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine protein kinases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2964
Polymers77,7181
Non-polymers5783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.663, 42.741, 175.327
Angle α, β, γ (deg.)90.000, 95.311, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 125 through 208 or resid 217...
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ARGMETA3 - 86
d_12ens_1GLYILEA95 - 339
d_13ens_1GLNLEUA341 - 368
d_14ens_1ALAARGA374 - 671
d_21ens_1ARGARGB1 - 655

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Components

#1: Protein Serine/threonine protein kinases


Mass: 77717.570 Da / Num. of mol.: 2
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-MAP / MAGNESIUM-5'-ADENYLY-IMIDO-TRIPHOSPHATE


Mass: 529.493 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16MgN6O12P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 910 / 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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 100 mM Tris-HCl, 17% w/v PEG 20 k, 100 mM MgCl2, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.2→46.68 Å / Num. obs: 78954 / % possible obs: 99.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.29 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.054 / Rrim(I) all: 0.102 / Net I/σ(I): 9.9
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2 / Num. unique obs: 4080 / CC1/2: 0.675 / Rpim(I) all: 0.374 / Rrim(I) all: 0.64

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y0X, 2PZI

4y0x

2pzi


Resolution: 2.2→43.02 Å / SU ML: 0.3042 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5355
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2457 4029 5.1 %
Rwork0.2093 74908 -
obs0.2111 78937 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.76 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10369 0 68 910 11347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002310656
X-RAY DIFFRACTIONf_angle_d0.562414500
X-RAY DIFFRACTIONf_chiral_restr0.04141656
X-RAY DIFFRACTIONf_plane_restr0.00421874
X-RAY DIFFRACTIONf_dihedral_angle_d13.42243984
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.36260955474 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.38951110.33192335X-RAY DIFFRACTION89.27
2.23-2.250.32621450.28272418X-RAY DIFFRACTION93.4
2.25-2.280.33941280.27232466X-RAY DIFFRACTION97.48
2.28-2.310.32371420.26992555X-RAY DIFFRACTION99.93
2.31-2.340.27741430.25322581X-RAY DIFFRACTION100
2.34-2.380.28241300.24762658X-RAY DIFFRACTION99.89
2.38-2.410.28521410.23672545X-RAY DIFFRACTION99.81
2.41-2.450.28431220.24172572X-RAY DIFFRACTION100
2.45-2.490.25171430.23482591X-RAY DIFFRACTION99.82
2.49-2.530.30231490.2452568X-RAY DIFFRACTION99.74
2.53-2.580.30771200.24442587X-RAY DIFFRACTION99.71
2.58-2.630.30951440.23542592X-RAY DIFFRACTION99.71
2.63-2.680.27621430.23682624X-RAY DIFFRACTION99.93
2.68-2.740.27491540.23532519X-RAY DIFFRACTION99.74
2.74-2.80.27461330.24012591X-RAY DIFFRACTION99.85
2.8-2.870.2751220.22112646X-RAY DIFFRACTION99.82
2.87-2.950.23861310.22932553X-RAY DIFFRACTION99.85
2.95-3.040.27911670.22522609X-RAY DIFFRACTION99.78
3.04-3.140.29251570.20912593X-RAY DIFFRACTION99.75
3.14-3.250.22251440.21312583X-RAY DIFFRACTION99.82
3.25-3.380.23271520.20742578X-RAY DIFFRACTION99.53
3.38-3.530.22451470.19872609X-RAY DIFFRACTION99.46
3.53-3.720.22671240.1852580X-RAY DIFFRACTION99.27
3.72-3.950.20731390.18422629X-RAY DIFFRACTION99.1
3.95-4.260.20061390.17412639X-RAY DIFFRACTION99.18
4.26-4.680.2021400.16622587X-RAY DIFFRACTION98.88
4.68-5.360.2121230.17462669X-RAY DIFFRACTION99.04
5.36-6.750.24991490.20112645X-RAY DIFFRACTION99.36
6.75-43.020.19541470.19122786X-RAY DIFFRACTION99.12
Refinement TLS params.Method: refined / Origin x: -23.2340740934 Å / Origin y: -5.34186423319 Å / Origin z: -43.4368659692 Å
111213212223313233
T0.120913441992 Å20.00516397101627 Å20.00319771687274 Å2-0.108634424688 Å20.00660437599898 Å2--0.121091867732 Å2
L0.0430886334854 °2-0.0125161487384 °20.0939522207743 °2-0.0302498283277 °2-0.00857186156543 °2--0.0731718428741 °2
S-0.00511233940839 Å °0.0278313417827 Å °-0.00385010899909 Å °-0.0248665764194 Å °-0.00220927651128 Å °-0.00580421607353 Å °-0.00743217227778 Å °0.0431985705837 Å °-9.89425033854E-6 Å °
Refinement TLS groupSelection details: all

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