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- PDB-3mky: Structure of SopB(155-323)-18mer DNA complex, I23 form -

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Basic information

Entry
Database: PDB / ID: 3mky
TitleStructure of SopB(155-323)-18mer DNA complex, I23 form
Components
  • DNA (5'-D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3')
  • Protein sopB
KeywordsDNA BINDING PROTEIN/DNA / partition / F plasmid / sopB / centromere / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


plasmid partitioning / DNA binding
Similarity search - Function
SopB, HTH domain / Centromere-binding protein HTH domain / Arc Repressor Mutant, subunit A - #2830 / ParB/RepB/Spo0J partition protein / ParB N-terminal domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein SopB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.86 Å
AuthorsSchumacher, M.A. / Piro, K. / Xu, W.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Insight into F plasmid DNA segregation revealed by structures of SopB and SopB-DNA complexes.
Authors: Schumacher, M.A. / Piro, K.M. / Xu, W.
History
DepositionApr 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 21, 2015Group: Database references / Structure summary
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
U: DNA (5'-D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3')
T: DNA (5'-D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3')
B: Protein sopB
P: Protein sopB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,65514
Polymers52,6944
Non-polymers96110
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
P: Protein sopB
hetero molecules

U: DNA (5'-D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3')
T: DNA (5'-D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3')
B: Protein sopB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,65514
Polymers52,6944
Non-polymers96110
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation23_555y+1/2,-z+1/2,-x+1/21
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-180 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.780, 200.780, 200.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
DetailsSopB(155-323) forms a primary dimer on the palindromic DNA and secondary dimer between DNA sites.

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Components

#1: DNA chain DNA (5'-D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3')


Mass: 5517.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The DNA was chemically synthesized.
#2: Protein Protein sopB / Plasmid partition protein B


Mass: 20829.646 Da / Num. of mol.: 2 / Fragment: UNP residues 155 to 323
Source method: isolated from a genetically manipulated source
Details: artificial gene / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: B, ECOK12F047, plasmid, sopB / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62558
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4

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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: 6.4 Å3/Da / Density % sol: 80.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.3 M ammonium sulphate, 0.1 M Tris pH 8.5 , 25% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 12, 2008 / Details: mirrors
RadiationMonochromator: gaphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.86→141 Å / Num. all: 30600 / Num. obs: 30569 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 104.5 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 12.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.86→63.49 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1278407.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.266 3067 10 %RANDOM
Rwork0.242 ---
all0.242 30569 --
obs0.242 30569 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.2856 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 71.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 2.86→63.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 732 50 0 2531
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d17.8
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_mcbond_it1.511.5
X-RAY DIFFRACTIONc_mcangle_it2.672
X-RAY DIFFRACTIONc_scbond_it3.112
X-RAY DIFFRACTIONc_scangle_it4.952.5
LS refinement shellResolution: 2.86→3.04 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.518 452 9.4 %
Rwork0.516 4346 -
obs--93.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dna-rna_rep.paramdna-rna.top

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