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- PDB-3gxq: Structure of ArtA and DNA complex -

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Basic information

Entry
Database: PDB / ID: 3gxq
TitleStructure of ArtA and DNA complex
Components
  • DNA (5'-D(*AP*CP*AP*TP*GP*AP*CP*AP*TP*G)-3')
  • DNA (5'-D(*AP*CP*AP*TP*GP*TP*CP*AP*TP*GP*T)-3')
  • Putative regulator of transfer genes ArtA
KeywordsDNA BINDING PROTEIN/DNA / ribbon-helix-helix / Plasmid / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Putative regulator of transfer genes ArtA / Antitoxin MazE
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus USA300 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsNi, L. / Firth, N. / Schumacher, M.A.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: The Staphylococcus aureus pSK41 plasmid-encoded ArtA protein is a master regulator of plasmid transmission genes and contains a RHH motif used in alternate DNA-binding modes.
Authors: Ni, L. / Jensen, S.O. / Ky Tonthat, N. / Berg, T. / Kwong, S.M. / Guan, F.H. / Brown, M.H. / Skurray, R.A. / Firth, N. / Schumacher, M.A.
History
DepositionApr 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative regulator of transfer genes ArtA
B: Putative regulator of transfer genes ArtA
C: DNA (5'-D(*AP*CP*AP*TP*GP*AP*CP*AP*TP*G)-3')
D: DNA (5'-D(*AP*CP*AP*TP*GP*TP*CP*AP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)18,8084
Polymers18,8084
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-56 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.830, 61.130, 40.500
Angle α, β, γ (deg.)90.00, 117.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative regulator of transfer genes ArtA


Mass: 6203.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus USA300 (bacteria)
Gene: ArtA, SAUSA300_pUSA030009 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q2FDC9, UniProt: A0A0H2XIU6*PLUS
#2: DNA chain DNA (5'-D(*AP*CP*AP*TP*GP*AP*CP*AP*TP*G)-3')


Mass: 3053.031 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*CP*AP*TP*GP*TP*CP*AP*TP*GP*T)-3')


Mass: 3348.209 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 10% PEG 2000, 0.1M Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 200011
2Acetate11
3PEG 200012
4Acetate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2008
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 1.98→61.08 Å / Num. obs: 6644 / % possible obs: 93.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.101 / Net I/σ(I): 11.5
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1213 / Rsym value: 0.351 / % possible all: 73.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementResolution: 2.35→35.98 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1114443.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 341 5.1 %RANDOM
Rwork0.237 ---
obs0.237 6644 96 %-
all-6920 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.9814 Å2 / ksol: 0.350224 e/Å3
Displacement parametersBiso mean: 44 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å20 Å212.46 Å2
2---13.48 Å20 Å2
3---15.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.35→35.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms863 425 0 36 1324
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 59 5.4 %
Rwork0.266 1035 -
obs-341 95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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