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- PDB-5x3r: Crystal structure of the SmcR complexed with QStatin -

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Basic information

Entry
Database: PDB / ID: 5x3r
TitleCrystal structure of the SmcR complexed with QStatin
ComponentsLuxR family transcriptional regulator
KeywordsDNA BINDING PROTEIN / Quorum sensing inhibitor
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
: / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1-(5-bromanylthiophen-2-yl)sulfonylpyrazole / Quorum-sensing regulator of virulence HapR
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJang, S.Y. / Hwang, J. / Kim, M.H.
CitationJournal: MBio / Year: 2018
Title: QStatin, a Selective Inhibitor of Quorum Sensing inVibrioSpecies
Authors: Kim, B.S. / Jang, S.Y. / Bang, Y.J. / Hwang, J. / Koo, Y. / Jang, K.K. / Lim, D. / Kim, M.H. / Choi, S.H.
History
DepositionFeb 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LuxR family transcriptional regulator
B: LuxR family transcriptional regulator
C: LuxR family transcriptional regulator
D: LuxR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,28710
Polymers95,9224
Non-polymers1,3656
Water8,323462
1
A: LuxR family transcriptional regulator
D: LuxR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6435
Polymers47,9612
Non-polymers6823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-28 kcal/mol
Surface area19660 Å2
MethodPISA
2
B: LuxR family transcriptional regulator
C: LuxR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6435
Polymers47,9612
Non-polymers6823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-34 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.669, 99.210, 129.407
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
LuxR family transcriptional regulator / SmcR / SmcR-like protein / VvpR


Mass: 23980.467 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: smcR, vvpR, JS86_16400 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L8G8
#2: Chemical
ChemComp-7Y3 / 1-(5-bromanylthiophen-2-yl)sulfonylpyrazole


Mass: 293.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H5BrN2O2S2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2M Li2SO4, 7% PEG3000, 0.1 M imidazole, pH 8.0

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Data collection

DiffractionMean temperature: 100.15 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: DIFFRACTOMETER / Date: Jul 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 59830 / % possible obs: 99.8 % / Redundancy: 14.5 % / Rsym value: 0.082 / Net I/σ(I): 53.54
Reflection shellResolution: 2.1→2.14 Å / % possible obs: 100 % / Redundancy: 14.7 % / Rsym value: 0.514

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KZ9

3kz9


Resolution: 2.1→35 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.4 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25794 3012 5 %RANDOM
Rwork0.1872 ---
obs0.19077 56748 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.312 Å2
Baniso -1Baniso -2Baniso -3
1--3.5 Å2-0 Å20 Å2
2--4.14 Å20 Å2
3----0.63 Å2
Refinement stepCycle: 1 / Resolution: 2.1→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6555 0 66 462 7083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0196756
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5251.959172
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5235801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.82924.085355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.301151122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1241556
X-RAY DIFFRACTIONr_chiral_restr0.1840.21031
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.025152
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.2722.7763216
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.4284.1414013
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.5143.2983540
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.28624.60110913
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.097→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 237 -
Rwork0.239 3974 -
obs--96.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7573-0.2927-0.13410.39630.37520.40530.0335-0.0051-0.02630.0239-0.0297-0.00020.0814-0.0214-0.00390.17010.03830.01170.0174-0.01220.12295.531-13.6127.444
20.82460.4482-0.26960.2687-0.23250.4762-0.03470.0369-0.1318-0.01090.0002-0.08270.09330.03060.03460.1550.01220.04330.01750.03710.193-24.083-14.75456.033
31.45020.3077-0.08230.2726-0.06560.0409-0.01340.21590.0509-0.0351-0.0176-0.04960.0351-0.04220.0310.1288-0.01910.01310.14350.00370.0705-37.7110.32442.744
41.6709-0.2573-0.19060.58590.19690.0876-0.0025-0.14950.0480.02040.00430.01710.01770.0599-0.00190.12380.0093-0.01950.17760.00330.027918.9151.53521.469
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 205
2X-RAY DIFFRACTION2B4 - 205
3X-RAY DIFFRACTION3C3 - 202
4X-RAY DIFFRACTION4D4 - 203

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