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- PDB-5j2y: Molecular insight into the regulatory mechanism of the quorum-sen... -

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Basic information

Entry
Database: PDB / ID: 5j2y
TitleMolecular insight into the regulatory mechanism of the quorum-sensing repressor RsaL in Pseudomonas aeruginosa
Components
  • (DNA (26-MER)) x 2
  • Regulatory proteinRegulation of gene expression
KeywordsGENE REGULATION/DNA / Quorum-sensing repressor / gene regulation / RsaL-DNA complex / GENE REGULATION-DNA complex
Function / homology
Function and homology information


: / positive regulation of single-species biofilm formation / negative regulation of elastin catabolic process / negative regulation of secondary metabolite biosynthetic process / quorum sensing / negative regulation of cell motility / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Regulatory protein RsaL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsZhao, J. / Gan, J. / Zhang, J. / Kang, H. / Kong, W. / Zhu, M. / Li, F. / Song, Y. / Qin, J. / Liang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation31000049 China
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Crystal structure of Pseudomonas aeruginosa RsaL bound to promoter DNA reaffirms its role as a global regulator involved in quorum-sensing.
Authors: Kang, H. / Gan, J. / Zhao, J. / Kong, W. / Zhang, J. / Zhu, M. / Li, F. / Song, Y. / Qin, J. / Liang, H.
History
DepositionMar 30, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _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
Revision 1.2Nov 15, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / struct_ref
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein
B: Regulatory protein
F: DNA (26-MER)
R: DNA (26-MER)
f: DNA (26-MER)
r: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)50,9346
Polymers50,9346
Non-polymers00
Water93752
1
A: Regulatory protein
F: DNA (26-MER)
r: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)25,4673
Polymers25,4673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Regulatory protein
R: DNA (26-MER)
f: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)25,4673
Polymers25,4673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.245, 52.983, 69.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 9 - 75 / Label seq-ID: 9 - 75

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Regulatory protein / Regulation of gene expression / Regulatory protein RsaL / RsaL protein / Uncharacterized protein / Virulence gene repressor RsaL


Mass: 9500.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: rsaL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9X7H4
#2: DNA chain DNA (26-MER)


Mass: 8001.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (26-MER)


Mass: 7965.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1.77 Å3/Da / Density % sol: 30.33 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Tris hydrochloride pH8.5, 30% Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 13851 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 1.6 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→39.93 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.82 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.957 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25182 735 5 %RANDOM
Rwork0.22361 ---
obs0.22499 13851 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.781 Å2
Baniso -1Baniso -2Baniso -3
1-2.39 Å20 Å2-0 Å2
2---1.88 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 2046 0 52 3185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0143421
X-RAY DIFFRACTIONr_bond_other_d0.0050.022180
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.4175052
X-RAY DIFFRACTIONr_angle_other_deg2.26235090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5585140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.97222.37359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64215182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8211513
X-RAY DIFFRACTIONr_chiral_restr0.0770.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022473
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02730
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3361 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.403→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 52 -
Rwork0.352 969 -
obs--98.65 %

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