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- PDB-6dql: Crystal structure of Regulator of Proteinase B RopB complexed with SIP -

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Basic information

Entry
Database: PDB / ID: 6dql
TitleCrystal structure of Regulator of Proteinase B RopB complexed with SIP
Components
  • Regulator of Proteinase B RopB
  • SpeB-inducing peptide (SIP)
KeywordsDNA BINDING PROTEIN / Streptococcus pyogenes / Regulator / virulence regulation / quorum sensing
Function / homologyTranscription activator MutR, C-terminal / HTH-type transcriptional regulator Rgg, C-terminal domain / : / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Tetratricopeptide-like helical domain superfamily / DNA binding / Putative transcription regulator
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsDo, H. / Makthal, N. / VanderWal, A.R. / Olsen, R.J. / Musser, J.M. / Kumaraswami, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI109096-01A1 United States
CitationJournal: Nat Commun / Year: 2019
Title: Environmental pH and peptide signaling control virulence of Streptococcus pyogenes via a quorum-sensing pathway.
Authors: Do, H. / Makthal, N. / VanderWal, A.R. / Saavedra, M.O. / Olsen, R.J. / Musser, J.M. / Kumaraswami, M.
History
DepositionJun 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulator of Proteinase B RopB
B: Regulator of Proteinase B RopB
C: SpeB-inducing peptide (SIP)


Theoretical massNumber of molelcules
Total (without water)56,7423
Polymers56,7423
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-34 kcal/mol
Surface area25380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.211, 94.211, 179.957
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 56 - 280 / Label seq-ID: 1 - 225

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Regulator of Proteinase B RopB


Mass: 27846.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: rgg / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D3KVD8
#2: Protein/peptide SpeB-inducing peptide (SIP)


Mass: 1048.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 4.14 Å3/Da / Density % sol: 70.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 2.7 M potassium formate, 0.1 M Tris pH 7.3, 1% PEG2000, 0.15 M potassium chloride and 1 mM EDTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 13969 / % possible obs: 99.5 % / Redundancy: 20 % / CC1/2: 1 / Rsym value: 0.065 / Net I/σ(I): 24.5
Reflection shellResolution: 3.3→3.41 Å / Num. unique obs: 13279 / CC1/2: 0.917 / Rsym value: 1.772

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DL2

5dl2


Resolution: 3.3→29.17 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.952 / SU B: 22.683 / SU ML: 0.4 / Cross valid method: THROUGHOUT / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26598 690 4.9 %RANDOM
Rwork0.23358 ---
obs0.23532 13279 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 174.789 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å20 Å2
2--1.87 Å20 Å2
3----3.74 Å2
Refinement stepCycle: 1 / Resolution: 3.3→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 0 13 3868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193931
X-RAY DIFFRACTIONr_bond_other_d0.0060.023735
X-RAY DIFFRACTIONr_angle_refined_deg1.0141.9535293
X-RAY DIFFRACTIONr_angle_other_deg1.19738591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1075458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.96425.122205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71915747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4081512
X-RAY DIFFRACTIONr_chiral_restr0.0570.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024393
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02951
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it12.15616.8731841
X-RAY DIFFRACTIONr_mcbond_other12.15516.871840
X-RAY DIFFRACTIONr_mcangle_it18.76325.3362296
X-RAY DIFFRACTIONr_mcangle_other18.75925.3392297
X-RAY DIFFRACTIONr_scbond_it13.21418.052089
X-RAY DIFFRACTIONr_scbond_other13.2118.0472089
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other19.94826.6012996
X-RAY DIFFRACTIONr_long_range_B_refined26.494995
X-RAY DIFFRACTIONr_long_range_B_other26.4894996
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 25280 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 73 -
Rwork0.21 975 -
obs--99.24 %

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