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- PDB-5w4n: Crystal structure of Streptococcus dysgalactiae SHP pheromone rec... -

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Basic information

Entry
Database: PDB / ID: 5w4n
TitleCrystal structure of Streptococcus dysgalactiae SHP pheromone receptor Rgg2(C45S)
ComponentsTranscriptional regulatorTranscriptional regulation
KeywordsDNA BINDING PROTEIN / DNA BINDING / PHEROMONE BINDING / REPEAT DOMAIN / QUORUM SENSING / RRNPP
Function / homologyHTH-type transcriptional regulator Rgg, C-terminal domain / Transcription activator MutR, C-terminal / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / Transcriptional regulator
Function and homology information
Biological speciesStreptococcus dysgalactiae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.198 Å
AuthorsNeiditch, M.B. / Khataokar, A.A. / Capodagli, G.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI125452 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Activating mutations in quorum-sensing regulator Rgg2 and its conformational flexibility in the absence of an intermolecular disulfide bond.
Authors: Wilkening, R.V. / Capodagli, G.C. / Khataokar, A. / Tylor, K.M. / Neiditch, M.B. / Federle, M.J.
History
DepositionJun 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator
B: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5398
Polymers67,0562
Non-polymers4836
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-15 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.368, 83.268, 129.295
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 Transcriptional regulator / Transcriptional regulation


Mass: 33527.914 Da / Num. of mol.: 2 / Mutation: C45A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus dysgalactiae (bacteria) / Gene: mutR / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J9X288
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 170 mM NH4OAc, 85 mM Na citrate (pH 5.6), 25.5% PEG 4,000, and 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 26, 2016
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.198→50 Å / Num. obs: 37790 / % possible obs: 98.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 45.29 Å2 / Rmerge(I) obs: 0.073 / Χ2: 28.116 / Net I/av σ(I): 34.1 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsΧ2% possible all
2.198-2.244.10.5462.918521.57998.6
2.24-2.2840.5011.84599
2.28-2.324.10.4391.76198.9
2.32-2.374.10.371.88498.8
2.37-2.424.10.3211.93899.1
2.42-2.484.10.2821.82598.8
2.48-2.544.10.2582.18398.6
2.54-2.614.10.2192.71199.4
2.61-2.694.10.1842.30699.3
2.69-2.774.10.1622.58798.9
2.77-2.874.10.1333.92699
2.87-2.994.10.1183.60699.2
2.99-3.124.10.1044.08499
3.12-3.294.20.0875.88899.3
3.29-3.494.10.0747.55899.1
3.49-3.764.10.06611.22698.8
3.76-4.1440.0611.44698.7
4.14-4.7440.05510.75698.5
4.74-5.9740.0670.05498.8
5.97-503.70.04414.93995.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YV6
Resolution: 2.198→35.559 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.75
RfactorNum. reflection% reflection
Rfree0.2327 1996 5.29 %
Rwork0.2049 --
obs0.2064 37727 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.2 Å2 / Biso mean: 54.5933 Å2 / Biso min: 28.32 Å2
Refinement stepCycle: final / Resolution: 2.198→35.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4556 0 26 89 4671
Biso mean--85.21 49.63 -
Num. residues----546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024668
X-RAY DIFFRACTIONf_angle_d0.3916280
X-RAY DIFFRACTIONf_chiral_restr0.033697
X-RAY DIFFRACTIONf_plane_restr0.002777
X-RAY DIFFRACTIONf_dihedral_angle_d5.1712800
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1985-2.25350.30631360.25752427256396
2.2535-2.31440.28361410.25372522266399
2.3144-2.38250.27611420.23562528267099
2.3825-2.45930.28881400.22782517265799
2.4593-2.54720.28271400.22652529266999
2.5472-2.64920.24581410.22022536267799
2.6492-2.76970.27821430.22452564270799
2.7697-2.91570.26321420.21752532267499
2.9157-3.09820.28941430.22242557270099
3.0982-3.33730.23661440.22672565270999
3.3373-3.67280.21991440.20512569271399
3.6728-4.20360.21721440.18372587273199
4.2036-5.29330.19291470.17782613276099
5.2933-35.5640.21251490.19892685283497
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0116-0.2620.22131.3031-0.46770.4984-0.00510.01240.072-0.0761-0.0741-0.0633-0.08020.02570.00010.4234-0.0008-0.00860.4170.02650.36625.96775.4294-34.9966
20.7411-0.07810.08581.44630.54020.3825-0.0551-0.02410.1889-0.404-0.01751.1293-0.137-0.0996-0.07630.28320.02690.02660.5229-0.07970.8426-21.4193-5.9578-19.0187
30.92080.08521.03451.29070.28512.0964-0.0208-0.0713-0.06870.0323-0.05030.07130.2425-0.1262-0.00030.3374-0.03290.05240.37040.0030.3205-5.397-16.5846-4.6049
40.26840.2054-0.5711.22250.29810.7525-0.1692-0.0183-0.0518-0.19480.0908-0.0104-0.08950.0040.00010.3957-0.0323-0.02020.3892-0.01630.3987-1.09-11.9759-36.48
51.42760.9929-1.12281.73570.04151.52480.10330.24750.28980.0691-0.2263-0.7361-0.1320.1619-0.00170.34360.0051-0.0870.4020.11050.525223.31055.2111-17.0889
60.9391-0.0778-0.2481.818-1.02451.62510.0529-0.07270.0640.3570.01250.0639-0.3946-0.0060.00010.423-0.0132-0.04990.3213-0.02060.33788.65568.26591.0758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 71 )A2 - 71
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 123 )A72 - 123
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 274 )A124 - 274
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 71 )B3 - 71
5X-RAY DIFFRACTION5chain 'B' and (resid 72 through 156 )B72 - 156
6X-RAY DIFFRACTION6chain 'B' and (resid 157 through 275 )B157 - 275

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