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- PDB-6hua: the competence regulator ComR from Streptococcus vestibularis in ... -

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Basic information

Entry
Database: PDB / ID: 6hua
Titlethe competence regulator ComR from Streptococcus vestibularis in complex with its cognate signaling peptide XIP
Components
  • Uncharacterized protein
  • XIP signaling peptide
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: 3.389 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: XIP signaling peptide
D: XIP signaling peptide


Theoretical massNumber of molelcules
Total (without water)74,8844
Polymers74,8844
Non-polymers00
Water00
1
A: Uncharacterized protein
C: XIP signaling peptide


Theoretical massNumber of molelcules
Total (without water)37,4422
Polymers37,4422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-18 kcal/mol
Surface area16520 Å2
MethodPISA
2
B: Uncharacterized protein
D: XIP signaling peptide


Theoretical massNumber of molelcules
Total (without water)37,4422
Polymers37,4422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-18 kcal/mol
Surface area12430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.190, 84.030, 152.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 36362.734 Da / Num. of mol.: 2
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: Protein/peptide XIP signaling peptide


Mass: 1079.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus vestibularis F0396 (bacteria)
Production host: synthetic construct (others)

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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: 3.02 Å3/Da / Density % sol: 59.33 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 5.5
Details: 12% PEG 4000, 0.1 M MgCl2, 0.1 M NaCl, 0.1 M tri-sodium citrate, 10 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 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.389→40 Å / Num. obs: 11266 / % possible obs: 99.7 % / Redundancy: 70.99 % / CC1/2: 0.999 / Rrim(I) all: 0.349 / Net I/σ(I): 15.16
Reflection shellResolution: 3.39→3.59 Å / Redundancy: 70.87 % / Mean I/σ(I) obs: 1.51 / Num. unique obs: 1748 / CC1/2: 0.72 / % possible all: 98.5

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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: 5JUB

5jub


Resolution: 3.389→38.873 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35.6
RfactorNum. reflection% reflection
Rfree0.301 563 5 %
Rwork0.2448 --
obs0.2477 11256 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 301.37 Å2 / Biso mean: 127.9374 Å2 / Biso min: 74.77 Å2
Refinement stepCycle: final / Resolution: 3.389→38.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4509 0 0 0 4509
Num. residues----541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024595
X-RAY DIFFRACTIONf_angle_d0.4936183
X-RAY DIFFRACTIONf_chiral_restr0.02682
X-RAY DIFFRACTIONf_plane_restr0.002781
X-RAY DIFFRACTIONf_dihedral_angle_d12.0941765
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3895-3.73030.42491370.31552603274099
3.7303-4.26950.28551390.255926332772100
4.2695-5.37690.28931400.250626672807100
5.3769-38.87590.28841470.222527902937100
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)
13.2829-0.2711-0.05263.73673.25045.79960.26531.2467-0.0576-1.3532-0.74570.71120.7793-0.20910.36122.15890.2481-0.4371.6257-0.10182.094336.989375.0655-30.1348
25.1828-0.6905-1.78334.1602-0.11356.74270.1050.45640.8541-0.1403-0.0301-0.3608-0.5399-0.0742-0.05330.92740.0023-0.05260.9380.1031.070427.209100.39213.4543
32.775-0.45670.43515.0485-1.49376.88770.09550.3667-0.33920.0058-0.20660.44230.486-0.43720.12551.0294-0.02450.02721.0456-0.15821.068617.878568.482213.0984
45.7732.6764-2.42274.5297-4.32394.13221.18970.87042.24151.66640.5029-0.1497-1.1975-0.5052-1.56631.11250.16090.0960.95040.0751.733730.1439100.023818.4452
57.75592.64774.62675.26423.23873.39181.07381.4999-0.55891.6505-0.55190.81891.39540.2319-0.4691.2755-0.16190.021.2035-0.14191.305714.475768.821718.2352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 75 )A4 - 75
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 300 )A76 - 300
3X-RAY DIFFRACTION3chain 'B' and (resid 72 through 300 )B72 - 300
4X-RAY DIFFRACTION4chain 'C' and (resid 17 through 24 )C17 - 24
5X-RAY DIFFRACTION5chain 'D' and (resid 17 through 24 )D17 - 24

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