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- PDB-7bhy: DNA-binding domain of DeoR in complex with the DNA operator -

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Basic information

Entry
Database: PDB / ID: 7bhy
TitleDNA-binding domain of DeoR in complex with the DNA operator
Components
  • DNA operator - strand 1
  • DNA operator - strand 2
  • Deoxyribonucleoside regulator
KeywordsDNA BINDING PROTEIN / Transcriptional repressor / Deoxyribose catabolism / Helix-turn-helix domain / Bacillus subtilis
Function / homology
Function and homology information


regulation of DNA-templated transcription initiation / cis-regulatory region sequence-specific DNA binding / carbohydrate 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 / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / Deoxyribonucleoside regulator
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNovakova, M. / Rezacova, P. / Skerlova, J. / Brynda, J.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Czech Republic)LO1304 Czech Republic
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family.
Authors: Soltysova, M. / Sieglova, I. / Fabry, M. / Brynda, J. / Skerlova, J. / Rezacova, P.
History
DepositionJan 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Data collection / Category: pdbx_seq_map_depositor_info / Item: _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: DNA operator - strand 1
G: DNA operator - strand 2
A: Deoxyribonucleoside regulator
B: Deoxyribonucleoside regulator
C: Deoxyribonucleoside regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2638
Polymers28,9785
Non-polymers2853
Water1,26170
1
E: DNA operator - strand 1
G: DNA operator - strand 2
A: Deoxyribonucleoside regulator
B: Deoxyribonucleoside regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4725
Polymers22,3774
Non-polymers951
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-34 kcal/mol
Surface area10940 Å2
MethodPISA
2
C: Deoxyribonucleoside regulator
hetero molecules

C: Deoxyribonucleoside regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5836
Polymers13,2032
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2010 Å2
ΔGint-29 kcal/mol
Surface area6880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.836, 96.836, 81.966
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11C-216-

HOH

21C-221-

HOH

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Components

#1: DNA chain DNA operator - strand 1


Mass: 4589.006 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: It differs from the original operator sequence by missing DT10.
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#2: DNA chain DNA operator - strand 2


Mass: 4585.038 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: It differs from the original operator sequence by missing DA6.
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#3: Protein Deoxyribonucleoside regulator


Mass: 6601.396 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: SNAAS sequence is a cloning artefact.
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: deoR, yxxC, BSU39430 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39140
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.38 Å3/Da / Density % sol: 63.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO4, 0.1 M Trizma base/bicine buffer system, pH 8.5, 12.5% (v/v) 2-methyl 2,4 pentanediol, 12.5% (v/v) PEG 1,000, and 12.5% (v/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2018
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→43.34 Å / Num. obs: 17897 / % possible obs: 99.6 % / Redundancy: 10.86 % / Biso Wilson estimate: 56.336 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.144 / Rrim(I) all: 0.151 / Χ2: 0.759 / Net I/σ(I): 14.08 / Num. measured all: 194360
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.448.1531.9521.0322853283428030.5522.08698.9
2.44-2.611.8731.3082.1331654267526660.811.36799.7
2.6-2.8111.5370.8413.3528786250224950.890.88199.7
2.81-3.0811.5240.5075.4126459230222960.9680.5399.7
3.08-3.4411.4850.20512.4224326212421180.9960.21599.7
3.44-3.9711.2760.124.2720995186718620.9980.10599.7
3.97-4.8510.9810.0732.9317679161416100.9990.07399.8
4.85-6.8310.9730.06137.8313980127512740.9990.06499.9
6.83-43.349.8680.02864.6876287807730.9990.0399.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W48

2w48


Resolution: 2.3→43.34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU R Cruickshank DPI: 0.2383 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 892 5 %RANDOM
Rwork0.2064 ---
obs0.2091 16949 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.72 Å2 / Biso mean: 54.464 Å2 / Biso min: 30.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 2.3→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 609 15 70 2048
Biso mean--83.07 51.38 -
Num. residues----195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122109
X-RAY DIFFRACTIONr_bond_other_d0.0310.0181706
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.4862979
X-RAY DIFFRACTIONr_angle_other_deg2.3371.883936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1455172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9952390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.28115272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4141512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022036
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02491
LS refinement shellResolution: 2.3→2.356 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.379 63 -
Rwork0.379 1209 -
obs--97.55 %

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