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- PDB-6fh3: Protein arginine kinase McsB in the pArg-bound state -

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Basic information

Entry
Database: PDB / ID: 6fh3
TitleProtein arginine kinase McsB in the pArg-bound 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
phospho-arginine / Protein-arginine kinase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 27, 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 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Jan 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)83,51512
Polymers82,5102
Non-polymers1,00510
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Native MS confirmed the dimer., light scattering, SEC-MALS confirmed the dimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint18 kcal/mol
Surface area29050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.000, 77.110, 94.130
Angle α, β, γ (deg.)90.00, 98.08, 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
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-RPI / phospho-arginine


Type: L-peptide linking / Mass: 254.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O5P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growMethod: 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. Soaked with 2 mM pArg.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.85→48.51 Å / Num. obs: 56542 / % possible obs: 95.04 % / Redundancy: 6.5 % / Net I/σ(I): 29.81
Reflection shellResolution: 1.85→1.92 Å

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M15

1m15


Resolution: 1.85→48.51 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.42
RfactorNum. reflection% reflection
Rfree0.2161 1998 3.55 %
Rwork0.1811 --
obs0.1823 56335 95.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5488 0 64 281 5833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085734
X-RAY DIFFRACTIONf_angle_d1.0197754
X-RAY DIFFRACTIONf_dihedral_angle_d18.8722208
X-RAY DIFFRACTIONf_chiral_restr0.056886
X-RAY DIFFRACTIONf_plane_restr0.0061018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8503-1.89660.5049830.45852268X-RAY DIFFRACTION56
1.8966-1.94790.35661360.27463698X-RAY DIFFRACTION91
1.9479-2.00520.23841440.22363934X-RAY DIFFRACTION97
2.0052-2.06990.27261480.19664020X-RAY DIFFRACTION99
2.0699-2.14390.20511480.18634013X-RAY DIFFRACTION99
2.1439-2.22970.22741480.18964025X-RAY DIFFRACTION98
2.2297-2.33120.20771480.19364018X-RAY DIFFRACTION99
2.3312-2.45410.27841480.18794003X-RAY DIFFRACTION99
2.4541-2.60780.24181480.18644037X-RAY DIFFRACTION99
2.6078-2.80920.24791470.18663993X-RAY DIFFRACTION99
2.8092-3.09180.21541500.19184051X-RAY DIFFRACTION98
3.0918-3.53910.19831490.17534056X-RAY DIFFRACTION99
3.5391-4.45840.19131500.15674093X-RAY DIFFRACTION99
4.4584-48.53060.19361510.17234128X-RAY DIFFRACTION99

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