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- PDB-6hu8: Apo form of the competence regulator ComR from Streptococcus vest... -

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Basic information

Entry
Database: PDB / ID: 6hu8
TitleApo form of the competence regulator ComR from Streptococcus vestibularis
ComponentsTranscriptional regulator ComR
KeywordsTRANSCRIPTION / RNPP family TPR domain HTH domain bacterial signaling peptide binding
Function / homologyComR, tetratricopeptide / ComR tetratricopeptide / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Tetratricopeptide-like helical domain superfamily / DNA binding / HTH cro/C1-type domain-containing protein
Function and homology information
Biological speciesStreptococcus vestibularis F0396 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.894 Å
AuthorsNessler, S. / Thuillier, J. / Ledesma, L. / Hols, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Molecular dissection of pheromone selectivity in the competence signaling system ComRS of streptococci.
Authors: Ledesma-Garcia, L. / Thuillier, J. / Guzman-Espinola, A. / Ensinck, I. / Li de la Sierra-Gallay, I. / Lazar, N. / Aumont-Nicaise, M. / Mignolet, J. / Soumillion, P. / Nessler, S. / Hols, P.
History
DepositionOct 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator ComR


Theoretical massNumber of molelcules
Total (without water)36,3631
Polymers36,3631
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.070, 38.290, 87.620
Angle α, β, γ (deg.)90.000, 113.200, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcriptional regulator ComR


Mass: 36362.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal Strep-tag sequence: GAGWSHPQFEK
Source: (gene. exp.) Streptococcus vestibularis F0396 (bacteria)
Gene: HMPREF9192_0126
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: E3CNF6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 7
Details: 20% PEG 3350, 0.15 M DL-malic acid, 20 mg/ml protein concentration

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.894→50 Å / Num. obs: 26937 / % possible obs: 99.1 % / Redundancy: 6.66 % / CC1/2: 0.998 / Rrim(I) all: 0.09 / Net I/σ(I): 11.8
Reflection shellResolution: 1.894→2.01 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.05 / Num. unique obs: 4162 / CC1/2: 0.55 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JUF

5juf


Resolution: 1.894→36.801 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.84
RfactorNum. reflection% reflection
Rfree0.2431 1347 5.01 %
Rwork0.21 --
obs0.2117 26903 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.49 Å2 / Biso mean: 45.5283 Å2 / Biso min: 27.38 Å2
Refinement stepCycle: final / Resolution: 1.894→36.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2467 0 0 56 2523
Biso mean---43.71 -
Num. residues----299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082508
X-RAY DIFFRACTIONf_angle_d13371
X-RAY DIFFRACTIONf_chiral_restr0.039376
X-RAY DIFFRACTIONf_plane_restr0.004428
X-RAY DIFFRACTIONf_dihedral_angle_d15.263976
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8937-1.96130.37151250.3672366249194
1.9613-2.03990.40131360.3432577271399
2.0399-2.13270.3641330.295625372670100
2.1327-2.24510.29451350.252525592694100
2.2451-2.38570.2861340.24625352669100
2.3857-2.56990.27431350.236125632698100
2.5699-2.82840.27071350.237425542689100
2.8284-3.23750.26921370.230226062743100
3.2375-4.07810.22151360.192125832719100
4.0781-36.80770.17891410.156626762817100

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