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- PDB-7oyk: DNA-binding domain of CggR in complex with the DNA operator -

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Basic information

Entry
Database: PDB / ID: 7oyk
TitleDNA-binding domain of CggR in complex with the DNA operator
Components
  • (DNA operator - strand ...) x 2
  • Central glycolytic genes regulator
KeywordsDNA BINDING PROTEIN / Transcriptional repressor / Glycolysis / Helix-turn-helix domain / Bacillus subtilis
Function / homology
Function and homology information


carbohydrate binding / DNA binding
Similarity search - Function
: / CggR N-terminal DNA binding domain / Sugar-binding domain, putative / : / Putative sugar-binding domain / NagB/RpiA transferase-like / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / Central glycolytic genes regulator
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Bacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.101 Å
AuthorsNovakova, M. / Rezacova, P. / Skerlova, J. / Brynda, J.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Ministry of Education (MoE, Czech Republic)LO1304 Czech Republic
Ministry of Education (MoE, Czech Republic)CZ.02.1.01/0.0/0.0/16_019/0000729 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
DepositionJun 24, 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 1.2Oct 16, 2024Group: Data collection / Derived calculations / Structure summary
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Central glycolytic genes regulator
DDD: Central glycolytic genes regulator
CCC: Central glycolytic genes regulator
BBB: Central glycolytic genes regulator
EEE: DNA operator - strand 1
FFF: DNA operator - strand 2
LLL: DNA operator - strand 1
KKK: DNA operator - strand 2
HHH: DNA operator - strand 2
GGG: DNA operator - strand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,20615
Polymers73,87410
Non-polymers3325
Water2,504139
1
AAA: Central glycolytic genes regulator
BBB: Central glycolytic genes regulator
EEE: DNA operator - strand 1
FFF: DNA operator - strand 2
hetero molecules


  • defined by author
  • Evidence: gel filtration, Two biological units binding the DNA duplex are present in the asymmetric unit. The first biological unit: protein chains A and B that bind DNA strands (chains) E and F. The ...Evidence: gel filtration, Two biological units binding the DNA duplex are present in the asymmetric unit. The first biological unit: protein chains A and B that bind DNA strands (chains) E and F. The second biological unit comprises two alternative conformers of the DNA duplex that differ only in the direction. Thus, this moiety contains: protein chains C and D and DNA chains K and L (dsDNA conformer A) and chains G and H (dsDNA conformer B).
  • 32.2 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)32,1746
Polymers32,0394
Non-polymers1352
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
DDD: Central glycolytic genes regulator
CCC: Central glycolytic genes regulator
LLL: DNA operator - strand 1
KKK: DNA operator - strand 2
HHH: DNA operator - strand 2
GGG: DNA operator - strand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0329
Polymers41,8356
Non-polymers1973
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.972, 103.141, 51.111
Angle α, β, γ (deg.)90.000, 90.537, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules AAADDDCCCBBB

#1: Protein
Central glycolytic genes regulator


Mass: 11121.280 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The first amino-acid residues "SNAAS" are remnants after the cleavage of the His-tag by TEV protease.
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: cggR, yvbQ, BSU33950 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O32253

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DNA operator - strand ... , 2 types, 6 molecules EEELLLGGGFFFKKKHHH

#2: DNA chain DNA operator - strand 1


Mass: 4885.209 Da / Num. of mol.: 3 / Source method: obtained synthetically
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#3: DNA chain DNA operator - strand 2


Mass: 4911.173 Da / Num. of mol.: 3 / Source method: obtained synthetically
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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Non-polymers , 4 types, 144 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% (w/v) PEG 3350, 100mM MES, pH 6.5, 100mM calcium chloride, 13% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2020
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 34417 / % possible obs: 96.8 % / Redundancy: 2.3 % / Biso Wilson estimate: 46.7 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.086 / Net I/σ(I): 9.4
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 10673 / CC1/2: 0.514 / Rrim(I) all: 1.111 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.101→45.837 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.183 / Average fsc free: 0.844 / Average fsc work: 0.8563 / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.216
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2527 1726 5.015 %
Rwork0.208 32691 -
all0.21 --
obs-32691 98.169 %
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: 43.543 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å2-0 Å2-0.007 Å2
2---0.002 Å2-0 Å2
3---0.003 Å2
Refinement stepCycle: LAST / Resolution: 2.101→45.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 1950 16 139 5150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125288
X-RAY DIFFRACTIONr_bond_other_d0.0280.0184275
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.4367534
X-RAY DIFFRACTIONr_angle_other_deg2.1921.9499909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.355387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5423.086162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22615603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.051524
X-RAY DIFFRACTIONr_chiral_restr0.0680.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024579
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021141
X-RAY DIFFRACTIONr_nbd_refined0.2090.2755
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2290.23198
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21820
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.21762
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2162
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0120.23
X-RAY DIFFRACTIONr_metal_ion_refined0.1580.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.210.232
X-RAY DIFFRACTIONr_nbd_other0.3560.2115
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2330.214
X-RAY DIFFRACTIONr_mcbond_it3.3144.3281542
X-RAY DIFFRACTIONr_mcbond_other3.3144.3261541
X-RAY DIFFRACTIONr_mcangle_it4.7056.4561925
X-RAY DIFFRACTIONr_mcangle_other4.7046.4581926
X-RAY DIFFRACTIONr_scbond_it4.2344.5393746
X-RAY DIFFRACTIONr_scbond_other4.2334.5393747
X-RAY DIFFRACTIONr_scangle_it6.3516.6895607
X-RAY DIFFRACTIONr_scangle_other6.356.695608
X-RAY DIFFRACTIONr_lrange_it8.28143.1955989
X-RAY DIFFRACTIONr_lrange_other8.2843.2015990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.101-2.1550.4041220.3972333X-RAY DIFFRACTION94.8243
2.155-2.2140.3431250.3362366X-RAY DIFFRACTION98.5364
2.214-2.2780.3421190.2982255X-RAY DIFFRACTION98.2616
2.278-2.3480.2711190.2882250X-RAY DIFFRACTION98.7495
2.348-2.4250.3031140.2642173X-RAY DIFFRACTION99.1761
2.425-2.510.2881100.252074X-RAY DIFFRACTION98.6896
2.51-2.6050.3181050.2591976X-RAY DIFFRACTION97.6995
2.605-2.7110.3051030.2421941X-RAY DIFFRACTION98.6963
2.711-2.8310.291990.2161869X-RAY DIFFRACTION98.4492
2.831-2.9690.261950.2071788X-RAY DIFFRACTION98.7415
2.969-3.1290.298890.2131699X-RAY DIFFRACTION99.1131
3.129-3.3180.256850.1871601X-RAY DIFFRACTION98.2517
3.318-3.5470.215780.1661482X-RAY DIFFRACTION96.5944
3.547-3.830.249750.1721418X-RAY DIFFRACTION99.2686
3.83-4.1930.207670.1621299X-RAY DIFFRACTION99.2012
4.193-4.6850.195620.1511181X-RAY DIFFRACTION98.6508
4.685-5.4040.241550.1731022X-RAY DIFFRACTION97.3779
5.404-6.6040.261470.219883X-RAY DIFFRACTION98.4127
6.604-9.280.175360.202688X-RAY DIFFRACTION98.2361
9.28-45.8370.21210.187393X-RAY DIFFRACTION96.2791

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