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- PDB-1zx4: Structure of ParB bound to DNA -

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Basic information

Entry
Database: PDB / ID: 1zx4
TitleStructure of ParB bound to DNA
Components
  • (parS-small DNA centromere site) x 2
  • Plasmid Partition par B protein
KeywordsCELL CYCLE / partition / P1 / plasmid
Function / homology
Function and homology information


ParB protein family, C-terminal / ParB family / ParB/RepB/Spo0J partition protein / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily
Similarity search - Domain/homology
CITRIC ACID / DNA / DNA (> 10) / Chromosome (Plasmid) partitioning protein
Similarity search - Component
Biological speciesEnterobacteria phage P1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.98 Å
AuthorsSchumacher, M.A. / Funnell, B.E.
CitationJournal: Nature / Year: 2005
Title: Structures of ParB bound to DNA reveal mechanism of partition complex formation.
Authors: Schumacher, M.A. / Funnell, B.E.
History
DepositionJun 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Structure summary / Category: struct_keywords
Item: _struct_keywords.pdbx_keywords / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
T: parS-small DNA centromere site
S: parS-small DNA centromere site
A: Plasmid Partition par B protein
B: Plasmid Partition par B protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1676
Polymers59,7834
Non-polymers3842
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.600, 154.600, 132.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Cell settinghexagonal
Space group name H-MP6222
DetailsParB(142-333) is a dimer

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Components

#1: DNA chain parS-small DNA centromere site


Mass: 7707.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: W-strand
#2: DNA chain parS-small DNA centromere site


Mass: 7649.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: C-strand
#3: Protein Plasmid Partition par B protein / P1 ParB / ParB


Mass: 22212.584 Da / Num. of mol.: 2 / Fragment: P1 ParB / Mutation: residues 142-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Gene: parb / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q38420
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.8 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium citrate, imidazole, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium citrate11
2imidazole12
3sodium citrate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.006 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 23, 2005 / Details: mirrors
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 2.98→65.9 Å / Num. all: 19627 / Num. obs: 18057 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 98 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.09 / Net I/σ(I): 7
Reflection shellResolution: 2.98→3.15 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3000 / Rsym value: 0.44 / % possible all: 92

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.98→50.61 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3864998.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 2086 12.2 %RANDOM
Rwork0.248 ---
all0.2481 18057 --
obs0.2481 18001 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 125.7 Å2 / ksol: 0.444336 e/Å3
Displacement parametersBiso mean: 89.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.3 Å23.57 Å20 Å2
2--4.3 Å20 Å2
3----8.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.98→50.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 1019 26 7 3897
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d1.27
X-RAY DIFFRACTIONc_mcbond_it2.781.5
X-RAY DIFFRACTIONc_mcangle_it4.652
X-RAY DIFFRACTIONc_scbond_it5.22
X-RAY DIFFRACTIONc_scangle_it8.142.5
LS refinement shellResolution: 2.98→3.15 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 274 12.6 %
Rwork0.284 1902 -
obs--73.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5cit_xplor_par.txtcit_xplor_top.txt

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