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- PDB-8fk2: The N-terminal VicR from Streptococcus mutans -

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Basic information

Entry
Database: PDB / ID: 8fk2
TitleThe N-terminal VicR from Streptococcus mutans
ComponentsPutative response regulator CovR VicR-like protein
KeywordsGENE REGULATION / gene regulator
Function / homology
Function and homology information


DNA-binding transcription repressor activity / phosphorelay signal transduction system / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription
Similarity search - Function
: / OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain ...: / OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcriptional regulatory protein WalR
Similarity search - Component
Biological speciesStreptococcus mutans UA159 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsZhang, H. / Wu, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)5R01DE022350-10 United States
CitationJournal: Mbio / Year: 2023
Title: Small Molecule Attenuates Bacterial Virulence by Targeting Conserved Response Regulator.
Authors: Liu, C. / Zhang, H. / Peng, X. / Blackledge, M.S. / Furlani, R.E. / Li, H. / Su, Z. / Melander, R.J. / Melander, C. / Michalek, S. / Wu, H.
History
DepositionDec 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative response regulator CovR VicR-like protein
B: Putative response regulator CovR VicR-like protein


Theoretical massNumber of molelcules
Total (without water)27,5842
Polymers27,5842
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint1 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.032, 53.032, 196.290
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Putative response regulator CovR VicR-like protein


Mass: 13791.835 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans UA159 (bacteria) / Gene: covR, SMU_1517 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6L8Z5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 7.0, 20% PEG 3350, 0.1M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→41.6 Å / Num. obs: 12917 / % possible obs: 92.41 % / Redundancy: 3.8 % / Biso Wilson estimate: 40.98 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 26.736
Reflection shellResolution: 2.29→2.37 Å / Rmerge(I) obs: 0.32 / Num. unique obs: 1189

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→41.6 Å / SU ML: 0.2283 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 28.3789
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.259 1289 9.99 %
Rwork0.199 11610 -
obs0.2049 12899 92.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.66 Å2
Refinement stepCycle: LAST / Resolution: 2.29→41.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 0 76 2010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921960
X-RAY DIFFRACTIONf_angle_d1.08212638
X-RAY DIFFRACTIONf_chiral_restr0.0558306
X-RAY DIFFRACTIONf_plane_restr0.0098340
X-RAY DIFFRACTIONf_dihedral_angle_d5.9194258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.390.22611330.19181211X-RAY DIFFRACTION86.38
2.39-2.490.25551450.18791255X-RAY DIFFRACTION91.68
2.49-2.630.25851430.2051303X-RAY DIFFRACTION92.57
2.63-2.790.30141470.21861327X-RAY DIFFRACTION94.25
2.79-30.25891530.21111325X-RAY DIFFRACTION97.56
3.01-3.310.24341480.21791388X-RAY DIFFRACTION97.83
3.31-3.790.28711440.20851297X-RAY DIFFRACTION93.09
3.79-4.760.23071290.17191196X-RAY DIFFRACTION85.59
4.77-41.60.26641470.19871308X-RAY DIFFRACTION93.09
Refinement TLS params.Method: refined / Origin x: 21.5326909528 Å / Origin y: 48.8139720413 Å / Origin z: -16.3425510906 Å
111213212223313233
T0.395218093712 Å2-0.107796462747 Å20.00536671635877 Å2-0.27586568307 Å20.029140325473 Å2--0.298101651387 Å2
L1.46778599687 °20.420232313538 °20.061369087714 °2-1.50498461914 °20.19589563162 °2--1.4394190888 °2
S0.103652150406 Å °-0.102560122213 Å °0.0245032039692 Å °-0.0529604089216 Å °0.00581022816461 Å °0.0400193348634 Å °-0.0123208127311 Å °-0.000454389025121 Å °7.36128386287E-5 Å °
Refinement TLS groupSelection details: all

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