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- PDB-8wtb: Crystal structure of McsA/McsB complex truncated by chymotrypsin -

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Basic information

Entry
Database: PDB / ID: 8wtb
TitleCrystal structure of McsA/McsB complex truncated by chymotrypsin
Components
  • Protein-arginine kinase
  • Protein-arginine kinase activator protein
KeywordsTRANSFERASE / protein-arginine kinase / zinc-coordination motif / 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 / proteolysis / extracellular space / 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 / SAD / Resolution: 2.9 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
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)126,0956
Polymers125,9644
Non-polymers1312
Water00
1
A: Protein-arginine kinase
B: Protein-arginine kinase activator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0473
Polymers62,9822
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-10 kcal/mol
Surface area16660 Å2
MethodPISA
2
C: Protein-arginine kinase
D: Protein-arginine kinase activator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0473
Polymers62,9822
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-9 kcal/mol
Surface area16930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.869, 75.590, 79.190
Angle α, β, γ (deg.)90.00, 99.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein-arginine kinase


Mass: 41782.941 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
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.37 % / Description: Plate shape
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: 8.25% PEG 400, 6.6% PEG 3350, 0.1 M MgCl2, 0.1 M Tris/HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.9→88.63 Å / Num. obs: 22473 / % possible obs: 96.2 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 8.1
Reflection shellResolution: 2.9→3.08 Å / Rmerge(I) obs: 1.124 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3682

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Processing

Software
NameVersionClassification
PHENIX(1.19rc5_4047: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→88.63 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 1103 4.92 %
Rwork0.2052 --
obs0.2079 22408 95.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→88.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5286 0 2 0 5288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015368
X-RAY DIFFRACTIONf_angle_d1.1647226
X-RAY DIFFRACTIONf_dihedral_angle_d6.198712
X-RAY DIFFRACTIONf_chiral_restr0.06810
X-RAY DIFFRACTIONf_plane_restr0.01954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.46291280.38612729X-RAY DIFFRACTION97
3.03-3.190.36531340.27912620X-RAY DIFFRACTION96
3.19-3.390.31251380.24542602X-RAY DIFFRACTION94
3.39-3.650.31531140.24312663X-RAY DIFFRACTION95
3.65-4.020.24481340.18262700X-RAY DIFFRACTION97
4.02-4.60.20271500.15382611X-RAY DIFFRACTION94
4.6-5.80.21631380.17592727X-RAY DIFFRACTION97
5.8-88.630.23671670.18472653X-RAY DIFFRACTION94

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