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- PDB-3q5f: Crystal structure of the Salmonella transcriptional regulator Sly... -

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Basic information

Entry
Database: PDB / ID: 3q5f
TitleCrystal structure of the Salmonella transcriptional regulator SlyA in complex with DNA
Components
  • DNA (5'-D(*AP*AP*TP*AP*AP*CP*TP*TP*AP*GP*CP*AP*AP*GP*CP*TP*AP*AP*TP*TP*AP*TP*A)-3')
  • DNA (5'-D(*TP*TP*AP*TP*AP*AP*TP*TP*AP*GP*CP*TP*TP*GP*CP*TP*AP*AP*GP*TP*TP*AP*T)-3')
  • Transcriptional regulator slyA
KeywordsTRANSCRIPTION/DNA / MarR/SlyA protein family / winged helix-turn-helix / transcriptonal regulator / protein-DNA complex / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcriptional regulator, SlyA / Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Transcriptional regulator, SlyA / Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional regulator SlyA
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.96 Å
AuthorsDolan, K.T. / Duguid, E.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structures of SlyA Protein, a Master Virulence Regulator of Salmonella, in Free and DNA-bound States.
Authors: Dolan, K.T. / Duguid, E.M. / He, C.
History
DepositionDec 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator slyA
B: Transcriptional regulator slyA
C: DNA (5'-D(*AP*AP*TP*AP*AP*CP*TP*TP*AP*GP*CP*AP*AP*GP*CP*TP*AP*AP*TP*TP*AP*TP*A)-3')
D: DNA (5'-D(*TP*TP*AP*TP*AP*AP*TP*TP*AP*GP*CP*TP*TP*GP*CP*TP*AP*AP*GP*TP*TP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)47,6384
Polymers47,6384
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10800 Å2
ΔGint-79 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.566, 59.566, 291.177
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: SER / End label comp-ID: SER

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLUGLUCHAIN A OR CHAIN CAA2 - 1425 - 145
2SERSERCHAIN B OR CHAIN DBB3 - 1426 - 145

NCS oper: (Code: given
Matrix: (-0.81206, -0.582972, 0.026502), (-0.576007, 0.793414, -0.19675), (0.093672, -0.175038, -0.980096)
Vector: 21.8514, 33.825699, 258.697998)

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Components

#1: Protein Transcriptional regulator slyA / Cytolysin slyA / Salmolysin


Mass: 16761.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Strain: enterica serovar Typhimurium / Gene: slyA, STM1444 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40676
#2: DNA chain DNA (5'-D(*AP*AP*TP*AP*AP*CP*TP*TP*AP*GP*CP*AP*AP*GP*CP*TP*AP*AP*TP*TP*AP*TP*A)-3')


Mass: 7055.625 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*TP*AP*TP*AP*AP*TP*TP*AP*GP*CP*TP*TP*GP*CP*TP*AP*AP*GP*TP*TP*AP*T)-3')


Mass: 7059.592 Da / Num. of mol.: 1 / Source method: obtained synthetically
Sequence detailsAUTHORS STATE THAT THE SEQUENCING EXPERIMENTS OF THE CLONES CONFIRMED THE CODING SEQUENCE AT THESE ...AUTHORS STATE THAT THE SEQUENCING EXPERIMENTS OF THE CLONES CONFIRMED THE CODING SEQUENCE AT THESE POSITIONS IS GAGCCG (CORRESPONDING TO GLU-PRO).

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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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.74
Details: 20% PEG 4000, 0.1M sodium chloride, 0.05M magnesium chloride, 0.1M cacodylate, 2% benzamidine hydrochloride, pH 6.74, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2sodium chloride11
3magnesium chloride11
4cacodylateCacodylic acid11
5benzamidine hydrochloride11
6PEG 400012
7sodium chloride12
8magnesium chloride12
9cacodylateCacodylic acid12
10benzamidine hydrochloride12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.20610, 1.25494, 1.25525
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 18, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.20611
21.254941
31.255251
ReflectionRedundancy: 14.9 % / Av σ(I) over netI: 35.32 / Number: 123915 / Rmerge(I) obs: 0.111 / Χ2: 2.02 / D res high: 4 Å / D res low: 50 Å / Num. obs: 8323 / % possible obs: 98.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
8.65096.710.0533.23214.7
6.848.69910.072.55815.5
5.976.8499.310.1272.07115.6
5.435.9799.410.1521.92515.4
5.045.4399.110.1781.77915.5
4.745.049910.1951.75915.3
4.54.749910.2151.71715
4.314.598.910.2311.74514.3
4.144.3199.210.2411.63613.7
44.149910.2871.65313.8
ReflectionResolution: 2.96→50 Å / Num. obs: 11205 / % possible obs: 94.4 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.081 / Χ2: 1.483 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.96-3.087.70.267051.169163.2
3.08-3.28.60.1479581.35183.1
3.2-3.3410.50.14711271.299196.9
3.34-3.5213.20.13711561.46199.5
3.52-3.7414.10.14611471.367199.6
3.74-4.0314.20.11211691.424199.7
4.03-4.4414.10.09111661.774199.8
4.44-5.0813.80.07111981.4171100
5.08-6.3913.50.06812271.5531100
6.39-5012.20.03613521.676199.1

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 5 Å / D res low: 1000 Å / FOM : 0.65 / Reflection: 2534
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
3 wavelength11118.32-17.2
3 wavelength12112.43-23.08
3 wavelength1317.7-11.69
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
131.9727.2488.98TA600.93
23.3329.04320.066TA600.52
30.24838.77727.48TA600.5
Phasing MAD shell
Resolution (Å)FOM Reflection
18.26-10000.7139
11.44-18.260.67229
8.91-11.440.68289
7.55-8.910.73318
6.66-7.550.68360
6.03-6.660.69383
5.54-6.030.61391
5.16-5.540.52425
Phasing dmFOM : 0.82 / FOM acentric: 0.83 / FOM centric: 0.78 / Reflection: 2522 / Reflection acentric: 1661 / Reflection centric: 861
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
14.3-46.0990.920.970.91263591
8.9-14.30.920.930.9378200178
7.1-8.90.880.910.84442281161
6.3-7.10.830.860.77431294137
5.4-6.30.780.810.68710522188
5-5.40.680.710.6435329106

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVE2.13phasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
JBluIce-EPICSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.96→46.099 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 0.12 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2662 1060 9.99 %
Rwork0.2135 --
obs0.2189 10606 89.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.148 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso max: 149.78 Å2 / Biso mean: 67.2251 Å2 / Biso min: 29.71 Å2
Baniso -1Baniso -2Baniso -3
1-13.9864 Å20 Å2-0 Å2
2--13.9864 Å2-0 Å2
3----27.9729 Å2
Refinement stepCycle: LAST / Resolution: 2.96→46.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2249 937 0 0 3186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083331
X-RAY DIFFRACTIONf_angle_d1.3544697
X-RAY DIFFRACTIONf_chiral_restr0.064551
X-RAY DIFFRACTIONf_plane_restr0.004436
X-RAY DIFFRACTIONf_dihedral_angle_d22.2811348
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1120X-RAY DIFFRACTIONPOSITIONAL0.04
12B1120X-RAY DIFFRACTIONPOSITIONAL0.04
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.96-3.08960.491750.314467775253
3.0896-3.25250.35121160.26381014113078
3.2525-3.45620.28951280.21591194132292
3.4562-3.72290.29861440.22761257140195
3.7229-4.09740.26881390.20941268140798
4.0974-4.68980.2321490.1851322147198
4.6898-5.90670.25711490.19481340148999
5.9067-46.10490.22161600.19711474163499

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