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- PDB-6fh1: Protein arginine kinase McsB in the apo state -

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Basic information

Entry
Database: PDB / ID: 6fh1
TitleProtein arginine kinase McsB in the apo state
ComponentsProtein-arginine kinase
KeywordsSIGNALING PROTEIN / protein kinase / protein arginine kinase / protein arginine phosphorylation / phospho-binding domain
Function / homology
Function and homology information


protein arginine kinase / phosphocreatine biosynthetic process / creatine kinase activity / protein kinase activity / phosphorylation / ATP binding
Similarity search - Function
Protein arginine kinase / 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. / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
FORMIC ACID / IMIDAZOLE / Protein-arginine kinase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSuskiewicz, M.J. / Heuck, A. / Vu, L.D. / Clausen, T.
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Structure of McsB, a protein kinase for regulated arginine phosphorylation.
Authors: Suskiewicz, M.J. / Hajdusits, B. / Beveridge, R. / Heuck, A. / Vu, L.D. / Kurzbauer, R. / Hauer, K. / Thoeny, V. / Rumpel, K. / Mechtler, K. / Meinhart, A. / Clausen, T.
History
DepositionJan 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,93425
Polymers82,5102
Non-polymers1,42423
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Native MS confirmed the dimeric assembly. Mutating the dimerisation interface (R273E) resulted in a monomer in native MS., light scattering, SEC-MALS confirmed the ...Evidence: mass spectrometry, Native MS confirmed the dimeric assembly. Mutating the dimerisation interface (R273E) resulted in a monomer in native MS., light scattering, SEC-MALS confirmed the dimeric assembly. Mutating the dimerisation interface (R273E) resulted in a monomer in SEC-MALS.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint61 kcal/mol
Surface area30070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.720, 83.410, 97.780
Angle α, β, γ (deg.)90.00, 98.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein-arginine kinase / protein arginine kinase McsB


Mass: 41255.207 Da / Num. of mol.: 2 / Mutation: delta356-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: mcsB / Plasmid: pET-21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DMM5, protein arginine kinase
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 25% v/v ethylene glycol, 75 mM MES-imidazole, 58 mM sodium formate, 58 mM ammonium acetate, 58 mM sodium citrate, 58 mM sodium potassium tartrate, 58 mM sodium oxamate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 85408 / % possible obs: 95.93 % / Redundancy: 2.7 % / Biso Wilson estimate: 31.73 Å2 / Net I/σ(I): 13.47
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.6 % / Num. unique obs: 8509 / % possible all: 96.58

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Processing

Software
NameVersionClassification
PHENIX(1.13rc1_2961: ???)refinement
Cootmodel building
Omodel building
ARP/wARPmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M15

1m15


Resolution: 1.7→42.954 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2000 2.36 %Random
Rwork0.194 ---
obs0.1947 84865 95.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→42.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5484 0 94 363 5941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075792
X-RAY DIFFRACTIONf_angle_d0.7537823
X-RAY DIFFRACTIONf_dihedral_angle_d18.4352229
X-RAY DIFFRACTIONf_chiral_restr0.056899
X-RAY DIFFRACTIONf_plane_restr0.0051026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74250.46181440.42215967X-RAY DIFFRACTION97
1.7425-1.78960.43091420.38945875X-RAY DIFFRACTION96
1.7896-1.84230.43231420.3695859X-RAY DIFFRACTION95
1.8423-1.90170.36371360.32165674X-RAY DIFFRACTION93
1.9017-1.96970.26731430.26445915X-RAY DIFFRACTION96
1.9697-2.04860.25071450.2196043X-RAY DIFFRACTION98
2.0486-2.14180.24791460.2166018X-RAY DIFFRACTION98
2.1418-2.25470.22651450.20496044X-RAY DIFFRACTION98
2.2547-2.3960.24171460.19726043X-RAY DIFFRACTION98
2.396-2.58090.23481450.20015995X-RAY DIFFRACTION97
2.5809-2.84060.23311430.1945900X-RAY DIFFRACTION96
2.8406-3.25160.21731380.1965755X-RAY DIFFRACTION93
3.2516-4.09610.21071390.16465739X-RAY DIFFRACTION92
4.0961-42.96790.16981460.15796038X-RAY DIFFRACTION96

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