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- PDB-6h48: A polyamorous repressor: deciphering the evolutionary strategy us... -

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Basic information

Entry
Database: PDB / ID: 6h48
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 / XRE family transcriptional regulator / Orf20
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Orf20


Theoretical massNumber of molelcules
Total (without water)11,5821
Polymers11,5821
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.357, 77.357, 37.318
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Orf20 / Stl


Mass: 11582.222 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, UniProt: A0A2S6DEV9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 40%PEG3350 0.1M Bis-Tris 0.2M Na-thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.2→66.993 Å / Num. obs: 6522 / % possible obs: 96.7 % / Redundancy: 18.4 % / CC1/2: 0.999 / Rpim(I) all: 0.027 / Rrim(I) all: 0.116 / Rsym value: 0.112 / Net I/av σ(I): 3.5 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.2-2.3216.71.0550.78430.2531.0861.05588.3
2.32-2.4619.70.6831.19130.1570.7010.683100
2.46-2.6319.50.461.68610.1060.4720.46100
2.63-2.8417.20.2682.47580.0640.2760.26892.3
2.84-3.1119.20.1923.17440.0450.1980.192100
3.11-3.4819.10.1413.96810.0330.1450.141100
3.48-4.0217.80.1135.15520.0270.1160.11392.6
4.02-4.9218.40.08475120.020.0860.084100
4.92-6.9617.60.0886.74150.0210.0910.088100
6.96-38.67916.60.0677.12430.0170.0690.06799.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
SOLVEphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.2→66.99 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.2484 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.198
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 292 4.5 %RANDOM
Rwork0.2484 ---
obs0.2491 6227 96.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 149.85 Å2 / Biso mean: 67.634 Å2 / Biso min: 31.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.38 Å20 Å2
2--0.75 Å20 Å2
3----2.45 Å2
Refinement stepCycle: final / Resolution: 2.2→66.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms665 0 0 19 684
Biso mean---67.9 -
Num. residues----77
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.019676
X-RAY DIFFRACTIONr_bond_other_d00.02677
X-RAY DIFFRACTIONr_angle_refined_deg1.0022.018902
X-RAY DIFFRACTIONr_angle_other_deg3.21531573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1925.19776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.75925.15233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67415145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.133153
X-RAY DIFFRACTIONr_chiral_restr0.0430.298
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02709
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02136
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 22 -
Rwork0.376 338 -
all-360 -
obs--76.27 %

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