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- PDB-6waf: Crystal Structure of SmcR N55I from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 6waf
TitleCrystal Structure of SmcR N55I from Vibrio vulnificus
ComponentsLuxR family transcriptional regulator
KeywordsTRANSCRIPTION / quorum-sensing / transcription factor / DNA-binding protein
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
Quorum-sensing regulator of virulence HapR
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.381 Å
AuthorsNewman, J.D. / Russell, M.M. / Gonzalez-Gutierrez, G. / van Kessel, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124698 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: The DNA binding domain of the Vibrio vulnificus SmcR transcription factor is flexible and binds diverse DNA sequences.
Authors: Newman, J.D. / Russell, M.M. / Fan, L. / Wang, Y.X. / Gonzalez-Gutierrez, G. / van Kessel, J.C.
History
DepositionMar 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
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
Revision 1.2Oct 18, 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,6824
Polymers47,4902
Non-polymers1922
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-27 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.568, 57.921, 78.108
Angle α, β, γ (deg.)90.00, 109.83, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-302-

SO4

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Components

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


Mass: 23745.047 Da / Num. of mol.: 2 / Mutation: N55I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria)
Gene: smcR, vvpR, CRN32_08135, CRN52_17705, D8T54_02235, D8T65_23975, JS86_16400
Production host: Escherichia coli (E. coli) / References: UniProt: Q9L8G8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN
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: 3.75 Å3/Da / Density % sol: 67.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M of Lithium Sulfate, 0.1 M Imidazole buffer pH 7.6-8 and 6-10% PEG3350
PH range: 7.6 - 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Dec 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 3.38→46.38 Å / Num. obs: 9974 / % possible obs: 98.9 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rpim(I) all: 0.09 / Rrim(I) all: 0.168 / Rsym value: 0.141 / Net I/σ(I): 6.4
Reflection shellResolution: 3.38→3.5 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2051 / CC1/2: 0.605 / Rpim(I) all: 0.815 / Rrim(I) all: 1.476 / Rsym value: 1.223 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.15_3459: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kz9

3kz9


Resolution: 3.381→46.375 Å / SU ML: 0.75 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.67
RfactorNum. reflection% reflection
Rfree0.2934 448 4.81 %
Rwork0.2685 --
obs0.2696 9318 92.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.381→46.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3198 0 10 0 3208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043266
X-RAY DIFFRACTIONf_angle_d0.74440
X-RAY DIFFRACTIONf_dihedral_angle_d1.0421524
X-RAY DIFFRACTIONf_chiral_restr0.045509
X-RAY DIFFRACTIONf_plane_restr0.005574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.381-3.650.49451300.41532539X-RAY DIFFRACTION80
3.8695-4.87430.29171720.29053109X-RAY DIFFRACTION98
4.8743-46.3750.22681460.21353222X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 9.4476 Å / Origin y: -13.5835 Å / Origin z: 25.9465 Å
111213212223313233
T0.88 Å2-0.0296 Å2-0.0518 Å2-1.0196 Å2-0.0313 Å2--0.8622 Å2
L2.6028 °2-0.8939 °20.4144 °2-1.921 °2-0.7394 °2--1.7708 °2
S0.1062 Å °-0.1915 Å °-0.137 Å °-0.0437 Å °0.1284 Å °0.0853 Å °-0.0766 Å °-0.3786 Å °-0.199 Å °
Refinement TLS groupSelection details: all

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