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- PDB-5w4m: Crystal structure of Streptococcus dysgalactiae SHP pheromone rec... -

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Basic information

Entry
Database: PDB / ID: 5w4m
TitleCrystal structure of Streptococcus dysgalactiae SHP pheromone receptor Rgg2(C45S)
ComponentsTranscriptional regulator
KeywordsDNA BINDING PROTEIN / DNA BINDING / PHEROMONE BINDING / REPEAT DOMAIN / QUORUM SENSING / RRNPP
Function / homology
Function and homology information


HTH-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
Similarity search - Domain/homology
: / THIOCYANATE ION / Transcriptional regulator
Similarity search - Component
Biological speciesStreptococcus dysgalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.388 Å
AuthorsCapodagli, G.C. / Neiditch, M.B.
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 1.2Nov 22, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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)66,91314
Polymers66,1672
Non-polymers74612
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-41 kcal/mol
Surface area26120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.982, 174.982, 57.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transcriptional regulator


Mass: 33083.520 Da / Num. of mol.: 2 / Mutation: C45S
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

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Non-polymers , 6 types, 107 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.36 Å3/Da / Density % sol: 63.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 350mM KSCN, 100mM Bis-Tris propane pH 7.75, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.1808 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 25, 2016
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 2.388→50 Å / Num. obs: 34868 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 52.72 Å2 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.042 / Rrim(I) all: 0.115 / Χ2: 1.643 / Net I/av σ(I): 20.4 / Net I/σ(I): 13.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.388-2.447.40.8283.417250.8070.3270.8911.237100
2.44-2.497.50.7110.8280.280.7641.294100
2.49-2.537.50.6230.8770.2450.671.352100
2.53-2.597.50.5320.9020.2090.5721.412100
2.59-2.647.50.4510.9160.1780.4851.514100
2.64-2.77.50.3840.940.1510.4131.655100
2.7-2.777.50.3360.9480.1320.3611.677100
2.77-2.857.50.2740.960.1080.2951.784100
2.85-2.937.50.2350.9720.0920.2531.866100
2.93-3.027.50.2080.9730.0810.2231.881100
3.02-3.137.50.1870.9790.0730.2011.726100
3.13-3.267.50.1610.9830.0630.1731.958100
3.26-3.417.50.1450.9820.0570.1561.955100
3.41-3.587.50.1310.9870.0520.1411.893100
3.58-3.817.50.1150.990.0450.1231.806100
3.81-4.17.50.1090.990.0430.1171.701100
4.1-4.527.50.0940.9940.0370.1011.646100
4.52-5.177.50.0830.9950.0330.091.581100
5.17-6.517.50.0750.9960.0290.081.528100
6.51-507.20.0670.9960.0270.0721.37599.6

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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

4yv6


Resolution: 2.388→43.745 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.84
RfactorNum. reflection% reflection
Rfree0.2242 1951 5.76 %
Rwork0.1931 --
obs0.1949 33900 96.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.68 Å2 / Biso mean: 65.5324 Å2 / Biso min: 34.06 Å2
Refinement stepCycle: final / Resolution: 2.388→43.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4586 0 37 95 4718
Biso mean--85.81 60.25 -
Num. residues----550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034739
X-RAY DIFFRACTIONf_angle_d0.4456379
X-RAY DIFFRACTIONf_chiral_restr0.034705
X-RAY DIFFRACTIONf_plane_restr0.003794
X-RAY DIFFRACTIONf_dihedral_angle_d4.3923979
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 (%)
2.3875-2.44720.29381150.26221964207985
2.4472-2.51340.31821350.25222180231592
2.5134-2.58730.30321290.24512172230193
2.5873-2.67080.2711290.24212202233195
2.6708-2.76630.27861430.24592263240696
2.7663-2.8770.28071410.24292319246098
2.877-3.00790.30711400.23962269240998
3.0079-3.16650.2261420.23852332247499
3.1665-3.36480.26211420.220123422484100
3.3648-3.62450.23621460.211623642510100
3.6245-3.9890.22191420.179123412483100
3.989-4.56570.18371470.150823722519100
4.5657-5.75020.19931490.166523962545100
5.7502-43.75280.18331510.16824332584100
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)
10.75310.4633-0.86071.3478-0.31140.96480.0059-0.14860.06-0.00330.09610.19930.2696-0.18280.00020.5286-0.10150.01540.64430.0220.5043-48.3442-35.9499-13.1676
22.88110.7194-0.64371.22280.72581.7511-0.12960.46530.4032-0.22710.28110.1915-0.0386-0.1356-0.00080.4940.00430.00410.57170.08990.5246-39.0802-20.1-42.4611
32.628-0.087-0.59181.0727-0.3981.0610.1504-0.1770.5260.1748-0.0218-0.0907-0.15480.169100.4304-0.05920.00080.4821-0.05920.5707-16.5871-18.9066-34.06
41.4837-1.7082-0.58272.20210.21681.0647-0.46960.3917-0.1245-0.74950.59470.20510.30440.7350.160.687-0.3613-0.03620.9535-0.12010.4133-12.1934-28.2558-47.2643
50.72-0.80210.26341.35550.20030.59350.24730.28280.4890.4360.22660.3157-0.0696-0.33410.00010.61530.03210.12290.61910.0010.6585-50.8758-15.5027-20.2337
60.1345-0.06160.10770.2669-0.39720.2790.12280.1380.25360.4397-0.2150.1507-0.54690.29390.0240.6469-0.13-0.03990.7418-0.05250.4946-27.5342-28.119-7.85
70.76890.3497-0.38840.97820.57961.7313-0.0045-0.0686-0.18670.09830.0841-0.02030.18820.0830.00010.49510.0033-0.00960.54-0.02180.4929-24.7016-46.8988-15.6079
81.11090.20090.04061.828-0.78060.3732-0.00490.0426-0.2524-0.1151-0.259-0.3134-0.03510.0895-0.01270.4528-0.01980.03320.5569-0.02680.6078-6.9988-43.5917-28.1013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 71 )A3 - 71
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 154 )A72 - 154
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 257 )A155 - 257
4X-RAY DIFFRACTION4chain 'A' and (resid 258 through 274 )A258 - 274
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 55 )B3 - 55
6X-RAY DIFFRACTION6chain 'B' and (resid 56 through 99 )B56 - 99
7X-RAY DIFFRACTION7chain 'B' and (resid 100 through 215 )B100 - 215
8X-RAY DIFFRACTION8chain 'B' and (resid 216 through 280 )B216 - 280

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