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- PDB-7p4a: Non-canonical Staphylococcus aureus pathogenicity island repression. -

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Basic information

Entry
Database: PDB / ID: 7p4a
TitleNon-canonical Staphylococcus aureus pathogenicity island repression.
Components
  • Sri
  • Stl
KeywordsDNA BINDING PROTEIN / Mobile Genetic Element / Repressor / SaPI / HTH domain
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 / Uncharacterized protein / Orf22
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.901 Å
AuthorsMiguel-Romero, L. / Alqasmi, M. / Bacarizo, J. / Tan, J.A. / Cogdell, R.J. / Chen, J. / Byron, O. / Christie, G.E. / Marina, A. / Penades, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S003835/1 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Non-canonical Staphylococcus aureus pathogenicity island repression.
Authors: Miguel-Romero, L. / Alqasmi, M. / Bacarizo, J. / Tan, J.A. / Cogdell, R.J. / Chen, J. / Byron, O. / Christie, G.E. / Marina, A. / Penades, J.R.
History
DepositionJul 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stl
E: Sri
B: Stl
D: Sri


Theoretical massNumber of molelcules
Total (without water)72,0644
Polymers72,0644
Non-polymers00
Water1448
1
A: Stl
E: Sri
B: Stl
D: Sri

A: Stl
E: Sri
B: Stl
D: Sri


Theoretical massNumber of molelcules
Total (without water)144,1288
Polymers144,1288
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Unit cell
Length a, b, c (Å)100.211, 100.211, 298.688
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Stl


Mass: 29751.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pPROEX-Hta / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O54475
#2: Protein Sri


Mass: 6279.946 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: E4U00_01835, G6X37_04850, G6Y24_00280, GO782_16265, GO810_08430, SAMEA103891454_02805
Plasmid: pPROEX-HTa / Production host: Escherichia coli (E. coli) / References: UniProt: A0A659I9D5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.4M Ammonium phosphate, 25% PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97936 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 2.9→86.76 Å / Num. obs: 20492 / % possible obs: 99.7 % / Redundancy: 5.9 % / CC1/2: 0.846 / Net I/σ(I): 14.2
Reflection shellResolution: 2.9→3.08 Å / Rmerge(I) obs: 0.049 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3215 / CC1/2: 0.951

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata scaling
iMOSFLMdata reduction
Cootmodel building
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.901→83.478 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.867 / WRfactor Rfree: 0.338 / WRfactor Rwork: 0.295 / SU B: 24.585 / SU ML: 0.467 / Average fsc free: 0.7994 / Average fsc work: 0.8208 / Cross valid method: THROUGHOUT / ESU R: 1.13 / ESU R Free: 0.472
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.3428 1063 5.19 %RANDOM
Rwork0.2985 19419 --
all0.301 ---
obs-20482 99.432 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 94.994 Å2
Baniso -1Baniso -2Baniso -3
1-2.692 Å21.346 Å20 Å2
2--2.692 Å2-0 Å2
3----8.732 Å2
Refinement stepCycle: LAST / Resolution: 2.901→83.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4204 0 0 8 4212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134277
X-RAY DIFFRACTIONr_bond_other_d0.0030.0163993
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.655758
X-RAY DIFFRACTIONr_angle_other_deg1.1991.5959192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0615511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66525.046216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70815764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.081159
X-RAY DIFFRACTIONr_chiral_restr0.0460.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024779
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02975
X-RAY DIFFRACTIONr_nbd_refined0.2060.2953
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.23605
X-RAY DIFFRACTIONr_nbtor_refined0.170.22050
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21771
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.283
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.219
X-RAY DIFFRACTIONr_nbd_other0.1830.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2460.21
X-RAY DIFFRACTIONr_mcbond_it7.75810.3652074
X-RAY DIFFRACTIONr_mcbond_other7.75810.3612073
X-RAY DIFFRACTIONr_mcangle_it12.00315.5182575
X-RAY DIFFRACTIONr_mcangle_other1215.5232576
X-RAY DIFFRACTIONr_scbond_it6.85210.5012203
X-RAY DIFFRACTIONr_scbond_other6.85310.4922201
X-RAY DIFFRACTIONr_scangle_it11.05915.5713183
X-RAY DIFFRACTIONr_scangle_other11.0615.5713183
X-RAY DIFFRACTIONr_lrange_it16.051118.6614787
X-RAY DIFFRACTIONr_lrange_other16.051118.5934786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.901-2.9760.392870.371384X-RAY DIFFRACTION99.2578
2.976-3.0570.376670.3321366X-RAY DIFFRACTION99.3759
3.057-3.1460.408660.3391339X-RAY DIFFRACTION99.3635
3.146-3.2430.388560.3181304X-RAY DIFFRACTION99.5608
3.243-3.3490.357720.31252X-RAY DIFFRACTION99.3994
3.349-3.4660.399750.3141200X-RAY DIFFRACTION99.5316
3.466-3.5970.346630.3261176X-RAY DIFFRACTION99.5981
3.597-3.7430.388570.3011128X-RAY DIFFRACTION99.6636
3.743-3.910.34630.2931094X-RAY DIFFRACTION99.7414
3.91-4.10.314630.2741035X-RAY DIFFRACTION99.637
4.1-4.3210.421560.2661009X-RAY DIFFRACTION99.5327
4.321-4.5830.266530.275955X-RAY DIFFRACTION99.4083
4.583-4.8980.25540.249878X-RAY DIFFRACTION99.5726
4.898-5.2890.303480.272852X-RAY DIFFRACTION99.3378
5.289-5.7920.402410.363788X-RAY DIFFRACTION99.5198
5.792-6.4720.404380.361715X-RAY DIFFRACTION99.6032
6.472-7.4660.457290.331648X-RAY DIFFRACTION99.1215
7.466-9.1270.378270.253567X-RAY DIFFRACTION99
9.127-12.8370.234300.214446X-RAY DIFFRACTION98.9605
12.837-83.4780.422180.456283X-RAY DIFFRACTION97.7273

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