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- PDB-6fh2: Protein arginine kinase McsB in the AMP-PN-bound state -

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Basic information

Entry
Database: PDB / ID: 6fh2
TitleProtein arginine kinase McsB in the AMP-PN-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 / extracellular space / 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 / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain ...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 / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
AMP PHOSPHORAMIDATE / Protein-arginine kinase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.1Feb 20, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Apr 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 1.3Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Apr 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 1.5Jan 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

Downloads & links

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Assembly

Deposited unit
A: Protein-arginine kinase
B: Protein-arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3099
Polymers82,5102
Non-polymers7997
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Native MS confirms the dimer., light scattering, SEC-MALS confirms the dimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint12 kcal/mol
Surface area29820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.340, 80.620, 97.250
Angle α, β, γ (deg.)90.00, 99.20, 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-AN2 / AMP PHOSPHORAMIDATE


Mass: 426.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N6O9P2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.36 Å3/Da / Density % sol: 47.9 %
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. Soaked with 10 mM ...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 10 mM magnesium AMPPNP, which apparently hydrolysed during the procedure to ADP.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.7→48 Å / Num. obs: 21210 / % possible obs: 99.76 % / Redundancy: 11.1 % / Biso Wilson estimate: 62.63 Å2 / Net I/σ(I): 15.99
Reflection shellResolution: 2.7→2.8 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_3126: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M15

1m15


Resolution: 2.7→47.999 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 1998 9.42 %
Rwork0.2318 --
obs0.2348 21213 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→47.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5174 0 51 33 5258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085297
X-RAY DIFFRACTIONf_angle_d0.9177146
X-RAY DIFFRACTIONf_dihedral_angle_d14.0952009
X-RAY DIFFRACTIONf_chiral_restr0.064824
X-RAY DIFFRACTIONf_plane_restr0.008931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6998-2.76730.36311430.32311369X-RAY DIFFRACTION99
2.7673-2.84220.3441390.32321339X-RAY DIFFRACTION100
2.8422-2.92580.33591410.3221375X-RAY DIFFRACTION100
2.9258-3.02020.34511420.30341354X-RAY DIFFRACTION100
3.0202-3.12810.34381420.29431364X-RAY DIFFRACTION99
3.1281-3.25330.34031420.28621365X-RAY DIFFRACTION100
3.2533-3.40140.3041420.26781372X-RAY DIFFRACTION100
3.4014-3.58060.29851420.24711357X-RAY DIFFRACTION100
3.5806-3.80490.27251450.24211385X-RAY DIFFRACTION100
3.8049-4.09850.23291410.22091361X-RAY DIFFRACTION100
4.0985-4.51070.21711440.19781382X-RAY DIFFRACTION100
4.5107-5.16280.25071430.19541376X-RAY DIFFRACTION100
5.1628-6.5020.25271440.23941392X-RAY DIFFRACTION100
6.502-48.00690.21541480.18741424X-RAY DIFFRACTION100

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