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- PDB-8r7y: Deoxyribonucleoside regulator DeoR in complex with the DNA operator -

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Basic information

Entry
Database: PDB / ID: 8r7y
TitleDeoxyribonucleoside regulator DeoR in complex with the DNA operator
Components
  • Deoxyribonucleoside regulator
  • OL18 DNA operator, strand 1
  • OL18 DNA operator, strand 2
KeywordsDNA BINDING PROTEIN / transcriptional repressor / protein-DNA complex / Bacillus subtilis
Function / homology
Function and homology information


carbohydrate binding / DNA binding / identical protein binding
Similarity search - Function
Homeodomain-like domain / Sugar-binding domain, putative / Putative sugar-binding domain / NagB/RpiA transferase-like / RNA polymerase sigma factor, region 3/4-like
Similarity search - Domain/homology
DNA / DNA (> 10) / Deoxyribonucleoside regulator
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsPachl, P. / Soltysova, M. / Rezacova, P.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Czech Republic)8J23FR035 Czech Republic
CitationJournal: Nucleic Acids Res / Year: 2024
Title: Structural characterization of two prototypical repressors of SorC family reveals tetrameric assemblies on DNA and mechanism of function.
Authors: Markéta Šoltysová / Jana Škerlová / Petr Pachl / Karel Škubník / Milan Fábry / Irena Sieglová / Martina Farolfi / Irina Grishkovskaya / Michal Babiak / Jiří Nováček / Libor ...Authors: Markéta Šoltysová / Jana Škerlová / Petr Pachl / Karel Škubník / Milan Fábry / Irena Sieglová / Martina Farolfi / Irina Grishkovskaya / Michal Babiak / Jiří Nováček / Libor Krásný / Pavlína Řezáčová /
Abstract: The SorC family of transcriptional regulators plays a crucial role in controlling the carbohydrate metabolism and quorum sensing. We employed an integrative approach combining X-ray crystallography ...The SorC family of transcriptional regulators plays a crucial role in controlling the carbohydrate metabolism and quorum sensing. We employed an integrative approach combining X-ray crystallography and cryo-electron microscopy to investigate architecture and functional mechanism of two prototypical representatives of two sub-classes of the SorC family: DeoR and CggR from Bacillus subtilis. Despite possessing distinct DNA-binding domains, both proteins form similar tetrameric assemblies when bound to their respective DNA operators. Structural analysis elucidates the process by which the CggR-regulated gapA operon is derepressed through the action of two effectors: fructose-1,6-bisphosphate and newly confirmed dihydroxyacetone phosphate. Our findings provide the first comprehensive understanding of the DNA binding mechanism of the SorC-family proteins, shedding new light on their functional characteristics.
History
DepositionNov 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyribonucleoside regulator
B: Deoxyribonucleoside regulator
C: Deoxyribonucleoside regulator
D: Deoxyribonucleoside regulator
E: OL18 DNA operator, strand 1
F: OL18 DNA operator, strand 2
G: OL18 DNA operator, strand 2
H: OL18 DNA operator, strand 1


Theoretical massNumber of molelcules
Total (without water)165,2398
Polymers165,2398
Non-polymers00
Water1448
1
A: Deoxyribonucleoside regulator
B: Deoxyribonucleoside regulator
G: OL18 DNA operator, strand 2
H: OL18 DNA operator, strand 1


Theoretical massNumber of molelcules
Total (without water)82,6204
Polymers82,6204
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-28 kcal/mol
Surface area35090 Å2
MethodPISA
2
C: Deoxyribonucleoside regulator
D: Deoxyribonucleoside regulator
E: OL18 DNA operator, strand 1
F: OL18 DNA operator, strand 2


Theoretical massNumber of molelcules
Total (without water)82,6204
Polymers82,6204
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-33 kcal/mol
Surface area34720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.672, 166.672, 331.697
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A

NCS domain segments:

Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 312 / Label seq-ID: 6 - 317

Dom-IDComponent-IDEns-ID
111
211
322
422

NCS ensembles :
IDDetails
1Global NCS restraints between domains: 1 2
2Global NCS restraints between domains: 3 4

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Components

#1: Protein
Deoxyribonucleoside regulator


Mass: 35796.676 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The N-terminal GIDPFT sequence is a cloning artefact.
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: deoR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39140
#2: DNA chain OL18 DNA operator, strand 1


Mass: 5519.612 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#3: DNA chain OL18 DNA operator, strand 2


Mass: 5506.630 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.22 Å3/Da / Density % sol: 70.6 % / Description: Thin needle-shaped crystal.
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: The volume ratio of the protein/DNA solution and precipitant solution - 1:2 Precipitant solution: 50 mM sodium cacodylate, pH 6.3, 75 mM CaCl2, 25 mM MgCl2, 3.5% (v/v) PEG 2K Crystal was ...Details: The volume ratio of the protein/DNA solution and precipitant solution - 1:2 Precipitant solution: 50 mM sodium cacodylate, pH 6.3, 75 mM CaCl2, 25 mM MgCl2, 3.5% (v/v) PEG 2K Crystal was cryo-protected by a quick soaking in 25% (v/v) glycerol.
Temp details: Grown in an air-conditioned room.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9141 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9141 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 32081 / % possible obs: 98.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 122.8 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.748 / Net I/σ(I): 4.86
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
3.6-3.810.3549120.1238.886196.4
3.81-4.080.5347630.2976.256198.9
4.08-4.40.9144630.5483.563199.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→48.924 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.901 / SU B: 91.089 / SU ML: 1.116 / Cross valid method: FREE R-VALUE / ESU R Free: 0.795
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.3328 1482 5.001 %
Rwork0.2655 28152 -
all0.269 --
obs-29634 99.2 %
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: 172.198 Å2
Baniso -1Baniso -2Baniso -3
1-1.194 Å20.597 Å20 Å2
2--1.194 Å2-0 Å2
3----3.873 Å2
Refinement stepCycle: LAST / Resolution: 3.7→48.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9792 1464 0 8 11264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01211591
X-RAY DIFFRACTIONr_ext_dist_refined_b0.040.004133
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.66915969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg20.2244.4611878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.901569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1279.461974
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.7359.724499
X-RAY DIFFRACTIONr_chiral_restr0.2030.2021874
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.028173
X-RAY DIFFRACTIONr_nbd_refined0.2530.25858
X-RAY DIFFRACTIONr_nbtor_refined0.3150.27943
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2354
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4210.2279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2290.222
X-RAY DIFFRACTIONr_paralell_plane_angle_deg4.8460.667
X-RAY DIFFRACTIONr_mcbond_it14.01217.0784984
X-RAY DIFFRACTIONr_mcangle_it22.76630.6646223
X-RAY DIFFRACTIONr_scbond_it15.77517.3916607
X-RAY DIFFRACTIONr_scangle_it25.46731.5579746
X-RAY DIFFRACTIONr_lrange_it36.36233.13453899
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: medium positional; mediume thermal / Weight Biso : 2 / Weight position: 0.5

Ens-IDDom-IDRms dev Biso (Å2)Rms dev position (Å)
1120.657250.70856
1220.657250.70856
2322.136130.75009
2422.136130.75009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.7-3.7960.4391040.44919790.44921470.8160.84797.01910.442
3.796-3.8990.4221040.44119650.4420940.8320.81698.80610.436
3.899-4.0110.4711000.40618970.40920230.8370.85698.71480.4
4.011-4.1340.436980.39218670.39419830.8140.86799.09230.389
4.134-4.2680.448960.37518340.37919400.8260.86399.48450.368
4.268-4.4170.402930.35717530.35918590.8180.88199.30070.346
4.417-4.5820.392890.33217050.33518030.8670.90599.50080.312
4.582-4.7680.408870.30116380.30617370.8910.92699.30920.282
4.768-4.9770.352830.30115910.30416790.9040.92999.70220.276
4.977-5.2180.355800.26115230.26616120.9120.94799.44170.231
5.218-5.4960.321770.24614450.2515250.9260.95799.80330.208
5.496-5.8250.382720.26213860.26814620.8970.95299.72640.222
5.825-6.2210.311700.25813110.26113820.9370.95799.92760.213
6.221-6.7110.317640.26712330.2712980.9320.95599.9230.223
6.711-7.3370.351600.20811370.21512000.9370.97199.750.167
7.337-8.180.257550.16910330.17310910.9580.9899.7250.139
8.18-9.4020.209490.1569400.1589950.9740.98499.3970.135
9.402-11.410.241430.1458100.1498530.9640.9871000.133
11.41-15.7150.208350.26610.26960.9770.981000.187
15.715-48.9240.396230.3164380.324660.9090.94298.9270.3

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