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- PDB-6h49: A polyamorous repressor: deciphering the evolutionary strategy us... -

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Basic information

Entry
Database: PDB / ID: 6h49
TitleA polyamorous repressor: deciphering the evolutionary strategy used by the phage-inducible chromosomal islands to spread in nature.
ComponentsOrf20
KeywordsSTRUCTURAL PROTEIN / SaPI / Repressor
Function / homologyHelix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / Orf20
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCiges-Tomas, J.R. / Alite, C. / Bowring, J.Z. / Donderis, J. / Penades, J.R. / Marina, A.
Funding support Spain, United Kingdom, 6items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78571-P Spain
Spanish Ministry of Economy and CompetitivenessFPU13/02880 Spain
Spanish Ministry of Economy and CompetitivenessBES-2014-068617 Spain
Medical Research Council (United Kingdom)MR/M003876/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N002873/1 United Kingdom
European Research CouncilERC-ADG/2014 670932 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: The structure of a polygamous repressor reveals how phage-inducible chromosomal islands spread in nature.
Authors: Rafael Ciges-Tomas, J. / Alite, C. / Humphrey, S. / Donderis, J. / Bowring, J. / Salvatella, X. / Penades, J.R. / Marina, A.
History
DepositionJul 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Derived calculations / Category: reflns_shell / struct_conn / Item: _reflns_shell.d_res_high / _reflns_shell.d_res_low
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Orf20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3503
Polymers18,1571
Non-polymers1922
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-20 kcal/mol
Surface area8430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.538, 34.553, 36.990
Angle α, β, γ (deg.)90.00, 95.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Orf20


Mass: 18157.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F0J8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium Sulfate, 0.1M Bis-Tris 5.5 pH, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.8→33.69 Å / Num. obs: 15780 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.984 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.094 / Rrim(I) all: 0.237 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.856.20.20811690.4810.9010.227100
8.05-33.695.80.162000.9520.0730.17799.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.24data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→33.64 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21582 760 4.8 %RANDOM
Rwork0.17155 ---
obs0.17363 15020 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.599 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.11 Å2
2--0.34 Å20 Å2
3----0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.8→33.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1204 0 10 85 1299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0141237
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171102
X-RAY DIFFRACTIONr_angle_refined_deg1.9681.671668
X-RAY DIFFRACTIONr_angle_other_deg1.6051.6442584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4515145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55123.90664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31815228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.992154
X-RAY DIFFRACTIONr_chiral_restr0.1330.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021359
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02237
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6681.2585
X-RAY DIFFRACTIONr_mcbond_other4.631.194584
X-RAY DIFFRACTIONr_mcangle_it4.8331.774729
X-RAY DIFFRACTIONr_mcangle_other4.8541.779730
X-RAY DIFFRACTIONr_scbond_it10.3011.793652
X-RAY DIFFRACTIONr_scbond_other10.3251.79643
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.9212.399927
X-RAY DIFFRACTIONr_long_range_B_refined11.34715.111480
X-RAY DIFFRACTIONr_long_range_B_other11.31114.7731460
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.798→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 50 -
Rwork0.189 1111 -
obs--99.57 %

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