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- PDB-8wtc: Crystal structure of McsB kinase domain complexed with McsA. -

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Basic information

Entry
Database: PDB / ID: 8wtc
TitleCrystal structure of McsB kinase domain complexed with McsA.
Components
  • Protein-arginine kinase
  • Protein-arginine kinase activator protein
KeywordsTRANSFERASE / Protein-arginine kinase / Zinc-coordination motifs / kinase activator
Function / homology
Function and homology information


protein arginine kinase / stress response to cadmium ion / phosphocreatine biosynthetic process / stress response to copper ion / creatine kinase activity / cobalt ion binding / cadmium ion binding / kinase activity / protein kinase activity / copper ion binding ...protein arginine kinase / stress response to cadmium ion / phosphocreatine biosynthetic process / stress response to copper ion / creatine kinase activity / cobalt ion binding / cadmium ion binding / kinase activity / protein kinase activity / copper ion binding / phosphorylation / proteolysis / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
YacH protein / Protein arginine kinase / UVR domain superfamily / UvrB/uvrC motif / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. ...YacH protein / Protein arginine kinase / UVR domain superfamily / UvrB/uvrC motif / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / UVR domain / UVR domain profile. / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Protein-arginine kinase activator protein / Protein-arginine kinase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsArifuzzaman, M. / Kwon, E. / Kim, D.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Structural insights into the regulation of protein-arginine kinase McsB by McsA.
Authors: Arifuzzaman, M. / Kwon, E. / Kim, D.Y.
History
DepositionOct 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-arginine kinase
B: Protein-arginine kinase activator protein
C: Protein-arginine kinase
D: Protein-arginine kinase activator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0346
Polymers96,9044
Non-polymers1312
Water0
1
A: Protein-arginine kinase
B: Protein-arginine kinase activator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5173
Polymers48,4522
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-8 kcal/mol
Surface area16760 Å2
MethodPISA
2
C: Protein-arginine kinase
D: Protein-arginine kinase activator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5173
Polymers48,4522
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-14 kcal/mol
Surface area16750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.104, 74.208, 79.935
Angle α, β, γ (deg.)90.00, 100.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein-arginine kinase


Mass: 27252.803 Da / Num. of mol.: 2 / Fragment: McsB kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: mcsB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37570
#2: Protein Protein-arginine kinase activator protein


Mass: 21198.955 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: mcsA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37569
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 2.83 Å3/Da / Density % sol: 56.5 % / Description: Plate shape
Crystal growTemperature: 293 K / Method: microbatch / pH: 9
Details: 2% v/v 1,4-dioxane, 10% w/v PEG20000, 3% w/v 1,6-hexanediol, 0.1 M BICINE pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 26019 / % possible obs: 95.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 16.6
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1202

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Processing

Software
NameVersionClassification
PHENIX(1.19rc5_4047: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→43.45 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2657 1970 7.69 %
Rwork0.2163 --
obs0.2201 25631 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→43.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5263 0 2 0 5265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115345
X-RAY DIFFRACTIONf_angle_d1.2247195
X-RAY DIFFRACTIONf_dihedral_angle_d6.386709
X-RAY DIFFRACTIONf_chiral_restr0.065803
X-RAY DIFFRACTIONf_plane_restr0.012953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.3461390.3071662X-RAY DIFFRACTION95
2.87-2.950.37031450.28771741X-RAY DIFFRACTION99
2.95-3.030.33181430.28381725X-RAY DIFFRACTION98
3.03-3.130.33591420.29251692X-RAY DIFFRACTION97
3.13-3.240.36081450.27281742X-RAY DIFFRACTION98
3.24-3.370.36821400.26171681X-RAY DIFFRACTION96
3.37-3.530.27171320.23891587X-RAY DIFFRACTION90
3.53-3.710.26721450.23431735X-RAY DIFFRACTION99
3.71-3.950.27381450.22241747X-RAY DIFFRACTION99
3.95-4.250.23911440.19951724X-RAY DIFFRACTION97
4.25-4.680.23361350.17561629X-RAY DIFFRACTION92
4.68-5.350.23311460.18211752X-RAY DIFFRACTION98
5.35-6.740.25271370.21471649X-RAY DIFFRACTION92
6.74-43.450.19911320.17081595X-RAY DIFFRACTION87

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