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- PDB-6s7l: Arbitrium receptor from a Bacillus subtilis Katmira33 phage -

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Basic information

Entry
Database: PDB / ID: 6s7l
TitleArbitrium receptor from a Bacillus subtilis Katmira33 phage
Components
  • Arbitrium receptor
  • GLY-ILE-VAL-ARG-GLY-ALA
KeywordsDNA BINDING PROTEIN / Arbitrium
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMarina, A. / Gallego del Sol, F.
Funding support Spain, United Kingdom, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBIO2016-78571-P Spain
Medical Research Council (United Kingdom)MR/M003876/1 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Insights into the mechanism of action of the arbitrium communication system in SPbeta phages.
Authors: Gallego Del Sol, F. / Quiles-Puchalt, N. / Brady, A. / Penades, J.R. / Marina, A.
History
DepositionJul 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / refine
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arbitrium receptor
C: GLY-ILE-VAL-ARG-GLY-ALA
B: Arbitrium receptor
D: GLY-ILE-VAL-ARG-GLY-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9956
Polymers91,8114
Non-polymers1842
Water19811
1
A: Arbitrium receptor
C: GLY-ILE-VAL-ARG-GLY-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9983
Polymers45,9062
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-7 kcal/mol
Surface area18720 Å2
MethodPISA
2
B: Arbitrium receptor
D: GLY-ILE-VAL-ARG-GLY-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9983
Polymers45,9062
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-6 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.703, 209.765, 140.254
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Arbitrium receptor


Mass: 45332.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide GLY-ILE-VAL-ARG-GLY-ALA


Mass: 572.679 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.8 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 2-6 0.2 M Potassium acetate 0.1 M MES 6.0 15 % v/v Pentaerythritol ethoxylate (15/4 EO/OH) 3 % v/v Jeffamine T-403

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→104.88 Å / Num. obs: 32018 / % possible obs: 99.8 % / Redundancy: 4.7 % / Net I/σ(I): 9.5
Reflection shellResolution: 2.6→2.74 Å / Num. unique obs: 4606

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S7I

6s7i


Resolution: 2.6→104.88 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.675 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 1618 5.1 %RANDOM
Rwork0.2138 30374 --
obs0.2155 31992 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.02 Å2 / Biso mean: 66.5337 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å2-0 Å2
2--4.2 Å20 Å2
3----4.76 Å2
Refinement stepCycle: LAST / Resolution: 2.6→104.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6434 0 12 11 6457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196560
X-RAY DIFFRACTIONr_bond_other_d00.026108
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.9668804
X-RAY DIFFRACTIONr_angle_other_deg3.819314240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4145780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.58825.449334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.78151278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.9381526
X-RAY DIFFRACTIONr_chiral_restr0.1510.2952
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027190
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021316
X-RAY DIFFRACTIONr_mcbond_it3.416.3223132
X-RAY DIFFRACTIONr_mcbond_other3.3926.3193131
X-RAY DIFFRACTIONr_mcangle_it5.4639.4733908
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 121 -
Rwork0.382 2201 -
all-2322 -
obs--99.53 %

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