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- PDB-9lth: Crystal structure of transcriptional regulator (NrpR) from Strept... -

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Basic information

Entry
Database: PDB / ID: 9lth
TitleCrystal structure of transcriptional regulator (NrpR) from Streptococcus salivarius K12
ComponentsTranscriptional regulator
KeywordsTRANSCRIPTION / Streptococcus salivarius K12 / Transcriptional regulator
Function / homologyTranscription activator MutR, C-terminal / HTH-type transcriptional regulator Rgg, C-terminal domain / : / 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 salivarius K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsDo, H. / Nguyen, D.l. / Kumaraswami, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI182870-01A1 United States
CitationJournal: J.Bacteriol. / Year: 2025
Title: Environmental pH controls antimicrobial production by human probiotic Streptococcus salivarius.
Authors: Nguyen, D.L. / Saha, S. / Thacharodi, A. / Singh, B.B. / Mitra, S. / Do, H. / Kumaraswami, M.
History
DepositionFeb 6, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 9, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)34,0911
Polymers34,0911
Non-polymers00
Water19811
1
A: Transcriptional regulator

A: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)68,1832
Polymers68,1832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6090 Å2
ΔGint-36 kcal/mol
Surface area25500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.747, 128.260, 72.630
Angle α, β, γ (deg.)90.000, 100.616, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Transcriptional regulator


Mass: 34091.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus salivarius K12 (bacteria)
Gene: RSSL_00023 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J7TTH6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.1 M Bis-Tris propane (pH 7.95), 0.7 M Sodium Citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9797 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.59→36.705 Å / Num. obs: 9474 / % possible obs: 97.4 % / Redundancy: 2.5 % / CC1/2: 0.99 / Net I/σ(I): 11.8
Reflection shellResolution: 2.59→2.71 Å / Num. unique obs: 2958 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→36.705 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.926 / SU B: 14.468 / SU ML: 0.303 / Cross valid method: FREE R-VALUE / ESU R Free: 0.364
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2659 458 4.834 %
Rwork0.1834 9016 -
all0.187 --
obs-9474 97.199 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 76.112 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.017 Å2
2--0.011 Å2-0 Å2
3---0.042 Å2
Refinement stepCycle: LAST / Resolution: 2.59→36.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 0 11 2389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132422
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162335
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.6313262
X-RAY DIFFRACTIONr_angle_other_deg1.2391.5765351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1275284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.2123.358137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89515463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7891512
X-RAY DIFFRACTIONr_chiral_restr0.0660.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02606
X-RAY DIFFRACTIONr_nbd_refined0.2040.2592
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.22201
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21230
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21098
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.257
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.190.242
X-RAY DIFFRACTIONr_nbd_other0.240.2127
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2480.211
X-RAY DIFFRACTIONr_mcbond_it6.7357.6891139
X-RAY DIFFRACTIONr_mcbond_other6.7067.6861138
X-RAY DIFFRACTIONr_mcangle_it9.57511.5331422
X-RAY DIFFRACTIONr_mcangle_other9.57611.5381423
X-RAY DIFFRACTIONr_scbond_it6.7378.4251279
X-RAY DIFFRACTIONr_scbond_other6.7348.4291280
X-RAY DIFFRACTIONr_scangle_it10.25812.3591839
X-RAY DIFFRACTIONr_scangle_other10.25512.3631840
X-RAY DIFFRACTIONr_lrange_it16.507146.95510040
X-RAY DIFFRACTIONr_lrange_other16.502146.92210038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.6570.399410.263675X-RAY DIFFRACTION97.019
2.657-2.730.359440.273618X-RAY DIFFRACTION98.806
2.73-2.8090.308250.282637X-RAY DIFFRACTION98.2196
2.809-2.8950.427360.268644X-RAY DIFFRACTION98.6938
2.895-2.990.265240.274581X-RAY DIFFRACTION98.6949
2.99-3.0950.313280.264598X-RAY DIFFRACTION98.4277
3.095-3.2110.37290.237561X-RAY DIFFRACTION98.4975
3.211-3.3420.364200.212539X-RAY DIFFRACTION98.0702
3.342-3.490.245270.184527X-RAY DIFFRACTION97.5352
3.49-3.660.324210.181475X-RAY DIFFRACTION98.2178
3.66-3.8570.287280.162486X-RAY DIFFRACTION99.2278
3.857-4.090.25250.163436X-RAY DIFFRACTION98.7152
4.09-4.3720.226230.134428X-RAY DIFFRACTION99.1209
4.372-4.720.215140.142388X-RAY DIFFRACTION98.5294
4.72-5.1680.205210.142363X-RAY DIFFRACTION98.7147
5.168-5.7730.265180.201337X-RAY DIFFRACTION99.4398
5.773-6.6570.324150.186276X-RAY DIFFRACTION97.3244
6.657-8.1310.161120.167244X-RAY DIFFRACTION97.3384
8.131-11.4080.20370.138130X-RAY DIFFRACTION66.5049
11.408-36.70500.2173X-RAY DIFFRACTION59.3496

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