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- PDB-3mkz: Structure of SopB(155-272)-18mer complex, P21 form -

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Basic information

Entry
Database: PDB / ID: 3mkz
TitleStructure of SopB(155-272)-18mer complex, P21 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 / SopB / F plasmid / 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/Sulfiredoxin 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 / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsSchumacher, M.A.
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 29, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_ref_seq_dif
Item: _pdbx_struct_assembly_prop.biol_id / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Protein sopB
B: Protein sopB
C: DNA (5'-D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3')
D: DNA (5'-D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3')
U: Protein sopB
Y: DNA (5'-D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3')
Z: DNA (5'-D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3')
N: Protein sopB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,30212
Polymers75,1428
Non-polymers1604
Water21612
1
A: Protein sopB
C: DNA (5'-D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3')
D: DNA (5'-D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3')
N: Protein sopB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6115
Polymers37,5714
Non-polymers401
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-41 kcal/mol
Surface area16980 Å2
MethodPISA
2
U: Protein sopB
Y: DNA (5'-D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3')
Z: DNA (5'-D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3')
hetero molecules

B: Protein sopB


Theoretical massNumber of molelcules
Total (without water)37,6917
Polymers37,5714
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area4920 Å2
ΔGint-57 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.380, 47.120, 118.230
Angle α, β, γ (deg.)90.00, 115.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein sopB / Plasmid partition protein B


Mass: 13267.931 Da / Num. of mol.: 4 / Fragment: UNP residues 155 to 272
Source method: isolated from a genetically manipulated source
Details: artificial gene of sopB / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: B, ECOK12F047, F plasmid, sopB / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62558
#2: 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.: 4 / Source method: obtained synthetically / Details: The DNA was chemically synthesized.
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.71 Å3/Da / Density % sol: 66.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, Calcium chloride 200 mM, pH 7.5, 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: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 12, 2009 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.98→99 Å / Num. all: 22300 / Num. obs: 22277 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 250 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 7.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MKW

3mkw


Resolution: 2.98→50.07 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 706163.06 / 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
Rfree0.264 2202 9.9 %RANDOM
Rwork0.213 ---
all0.213 22280 --
obs0.213 22266 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.4301 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 79.4 Å2
Baniso -1Baniso -2Baniso -3
1--24.71 Å20 Å2-3.21 Å2
2--0.24 Å20 Å2
3---24.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.98→50.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3419 1464 4 12 4899
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_improper_angle_d1.28
LS refinement shellResolution: 2.98→3.17 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.398 307 8.9 %
Rwork0.337 3136 -
obs--90.1 %
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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