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- PDB-6tv6: Octameric McsB from Bacillus subtilis. -

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Basic information

Entry
Database: PDB / ID: 6tv6
TitleOctameric McsB from Bacillus subtilis.
ComponentsProtein-arginine kinase
KeywordsTRANSFERASE / phosho-arginine-kinase
Function / homology
Function and homology information


protein arginine kinase / phosphocreatine biosynthetic process / creatine kinase activity / kinase activity / protein kinase activity / ATP binding / cytoplasm
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
Protein-arginine kinase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSuskiewicz, M.J. / Hajdusits, B. / Meinhart, A. / Clausen, T.
Funding support Austria, 1items
OrganizationGrant numberCountry
European Research Council (ERC)694978 Austria
CitationJournal: Elife / Year: 2021
Title: McsB forms a gated kinase chamber to mark aberrant bacterial proteins for degradation.
Authors: Hajdusits, B. / Suskiewicz, M.J. / Hundt, N. / Meinhart, A. / Kurzbauer, R. / Leodolter, J. / Kukura, P. / Clausen, T.
History
DepositionJan 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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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
C: Protein-arginine kinase
D: Protein-arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,5358
Polymers170,4374
Non-polymers974
Water2,108117
1
A: Protein-arginine kinase
B: Protein-arginine kinase
C: Protein-arginine kinase
D: Protein-arginine kinase
hetero molecules

A: Protein-arginine kinase
B: Protein-arginine kinase
C: Protein-arginine kinase
D: Protein-arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,06916
Polymers340,8758
Non-polymers1948
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)137.790, 147.640, 81.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein
Protein-arginine kinase


Mass: 42609.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: mcsB, yacI, BSU00850 / Production host: Escherichia coli (E. coli) / References: UniProt: P37570, protein arginine kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 200 mM Mg-acetate / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→43.9 Å / Num. obs: 58145 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 53.6 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.146 / Net I/σ(I): 13.6
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4251 / CC1/2: 0.561 / Rrim(I) all: 0.153 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.16refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FH1

6fh1


Resolution: 2.5→43.9 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2908 5 %random
Rwork0.195 ---
obs0.195 55411 99.8 %-
Displacement parametersBiso mean: 55.52 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11283 0 4 117 11404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008911443
X-RAY DIFFRACTIONf_angle_d1.082715428
X-RAY DIFFRACTIONf_chiral_restr0.06881743
X-RAY DIFFRACTIONf_plane_restr0.00642022
X-RAY DIFFRACTIONf_dihedral_angle_d13.50967082

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