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- PDB-8w39: Vibrio vulnificus SmcR bound to the inhibitor PTSP -

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Basic information

Entry
Database: PDB / ID: 8w39
TitleVibrio vulnificus SmcR bound to the inhibitor PTSP
ComponentsSmcR
KeywordsDNA BINDING PROTEIN / Inhibitor / transcription factor / quorum-sensing receptor
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
: / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
: / Quorum-sensing regulator of virulence HapR
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPaczkowski, J.E. / Brockley, M.W. / van Kessel, J.C.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM14436101 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124698 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM132066 United States
National Science Foundation (NSF, United States)DBI-175710 United States
CitationJournal: To Be Published
Title: Ligand binding determines proteolytic stability of Vibrio LuxR/HapR quorum sensing transcription factors
Authors: Rasal, T.A. / Mallery, C.P. / Brockley, M.W. / Brown, L.C. / Paczkowski, J.E. / van Kessel, J.C.
History
DepositionFeb 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: SmcR
A: SmcR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9824
Polymers46,3852
Non-polymers5972
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-2 kcal/mol
Surface area16570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.011, 64.654, 138.729
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 SmcR / VvpR / TetR/AcrR family transcriptional regulator


Mass: 23192.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria)
Gene: smcR, vvpR, CRN52_17705, D8T54_02235, D8T65_23975, I7730_19665, XM75_c12331, XM78_c12413
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9L8G8
#2: Chemical ChemComp-A1AFF / (3S)-3-phenyl-1-[(2R)-thiolane-2-sulfonyl]pyrazolidine


Mass: 298.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H18N2O2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.0 MgSO4, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jul 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→47.29 Å / Num. obs: 31260 / % possible obs: 99.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 15.1
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.217 / Num. unique obs: 2538

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
pointlessdata scaling
BUCCANEERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→43.178 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 2.35 / Phase error: 37.32 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2998 1567 5.03 %
Rwork0.2711 --
obs0.2726 31130 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→43.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 38 64 2898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012889
X-RAY DIFFRACTIONf_angle_d1.3033930
X-RAY DIFFRACTIONf_dihedral_angle_d9.7971706
X-RAY DIFFRACTIONf_chiral_restr0.061460
X-RAY DIFFRACTIONf_plane_restr0.008501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.16790.37821400.36582647X-RAY DIFFRACTION100
2.1679-2.24530.39121300.32762665X-RAY DIFFRACTION100
2.2453-2.33520.30681340.2972656X-RAY DIFFRACTION100
2.3352-2.44150.30061330.26462647X-RAY DIFFRACTION99
2.4415-2.57020.31721380.27432662X-RAY DIFFRACTION100
2.5702-2.73120.2691330.26532674X-RAY DIFFRACTION100
2.7312-2.94210.31221240.28372693X-RAY DIFFRACTION100
2.9421-3.2380.3651530.27452672X-RAY DIFFRACTION99
3.238-3.70640.3231530.25562687X-RAY DIFFRACTION100
3.7064-4.66880.25491670.24572707X-RAY DIFFRACTION100
4.6688-43.1780.28521620.27412853X-RAY DIFFRACTION99

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