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- PDB-2ntz: Structure of a ParB-DNA complex reveals a double B-box interaction -

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Basic information

Entry
Database: PDB / ID: 2ntz
TitleStructure of a ParB-DNA complex reveals a double B-box interaction
Components
  • 5'-D(*CP*GP*TP*GP*AP*AP*AP*TP*CP*GP*CP*CP*AP*CP*GP*A)-3'
  • 5'-D(*TP*CP*GP*TP*GP*GP*CP*GP*AP*TP*TP*TP*CP*AP*CP*G)-3'
  • ParB
KeywordsCELL CYCLE/DNA / partition / segregation / parb / para / CELL CYCLE-DNA COMPLEX
Function / homology
Function and homology information


ParB protein family, C-terminal / ParB family / ParB/RepB/Spo0J partition protein / ParB N-terminal domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Chromosome (Plasmid) partitioning protein
Similarity search - Component
Biological speciesEnterobacteria phage P1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsSchumacher, M.A. / Mansoor, A. / Funnell, B.E.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structure of a four-way bridged ParB-DNA complex provides insight into P1 segrosome assembly.
Authors: Schumacher, M.A. / Mansoor, A. / Funnell, B.E.
History
DepositionNov 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: 5'-D(*CP*GP*TP*GP*AP*AP*AP*TP*CP*GP*CP*CP*AP*CP*GP*A)-3'
W: 5'-D(*TP*CP*GP*TP*GP*GP*CP*GP*AP*TP*TP*TP*CP*AP*CP*G)-3'
E: 5'-D(*CP*GP*TP*GP*AP*AP*AP*TP*CP*GP*CP*CP*AP*CP*GP*A)-3'
U: 5'-D(*TP*CP*GP*TP*GP*GP*CP*GP*AP*TP*TP*TP*CP*AP*CP*G)-3'
A: ParB
B: ParB


Theoretical massNumber of molelcules
Total (without water)64,0506
Polymers64,0506
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.420, 144.420, 78.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 4892.194 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*CP*GP*TP*GP*GP*CP*GP*AP*TP*TP*TP*CP*AP*CP*G)-3'


Mass: 4905.176 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein ParB


Mass: 22227.596 Da / Num. of mol.: 2 / Fragment: 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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21(de3) / References: UniProt: Q38420
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: 3.66 Å3/Da / Density % sol: 66.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, MES 6.5, Magnesium chloride, sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2MES 6.511
3Magnesium chloride11
4sodium chloride11
5H2O11
6MPD12
7MES 6.512
8Magnesium chloride12
9sodium chloride12
10H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.989
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 23, 2004 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 3.35→129.1 Å / Num. all: 15990 / Num. obs: 15703 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 89 Å2 / Rsym value: 0.049 / Net I/σ(I): 7.8
Reflection shellResolution: 3.35→3.5 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2177 / Rsym value: 0.333 / % possible all: 94

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1zx4

1zx4


Resolution: 3.35→66.72 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 5132409.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.336 692 5 %RANDOM
Rwork0.288 ---
all0.29 15990 --
obs0.288 13749 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.6469 Å2 / ksol: 0.175069 e/Å3
Displacement parametersBiso mean: 145.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.1 Å213.58 Å20 Å2
2--4.1 Å20 Å2
3----8.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.14 Å
Refinement stepCycle: LAST / Resolution: 3.35→66.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2844 1300 0 0 4144
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d32.2
X-RAY DIFFRACTIONc_improper_angle_d2.94
LS refinement shellResolution: 3.35→3.56 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.389 109 4.8 %
Rwork0.356 2172 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top

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