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- PDB-3no7: Crystal structure of the centromere-binding protein ParB from pla... -

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Basic information

Entry
Database: PDB / ID: 3no7
TitleCrystal structure of the centromere-binding protein ParB from plasmid pCXC100
ComponentsPutative plasmid related protein
KeywordsDNA BINDING PROTEIN / Ribbon-helix-helix
Function / homologyArc Repressor Mutant - #30 / Centromere-binding protein ParB, C-terminal / Centromere-binding protein ParB C-terminal / Arc Repressor Mutant / Helix non-globular / Special / Putative plasmid related protein
Function and homology information
Biological speciesLeifsonia xyli subsp. cynodontis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.4 Å
AuthorsYe, K.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Crystal structure and centromere binding of the plasmid segregation protein ParB from pCXC100
Authors: Huang, L. / Yin, P. / Zhu, X. / Zhang, Y. / Ye, K.
History
DepositionJun 24, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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

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Assembly

Deposited unit
A: Putative plasmid related protein
B: Putative plasmid related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,99912
Polymers18,0382
Non-polymers96110
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-24 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.186, 74.186, 52.596
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-8-

SO4

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Components

#1: Protein Putative plasmid related protein / ParB


Mass: 9019.030 Da / Num. of mol.: 2 / Fragment: UNP residues 65-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leifsonia xyli subsp. cynodontis (bacteria)
Gene: pCXC100 / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q6EEF9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.8M Li2SO4, 0.01M MgSO4, 0.05M cacodylate-Na, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 33276 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 28
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 0.835 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21243 1672 5.1 %RANDOM
Rwork0.19742 ---
obs0.19818 31419 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.602 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 50 162 1187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211027
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0291.9771382
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0685117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.28721.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47815177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8721518
X-RAY DIFFRACTIONr_chiral_restr0.0690.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02768
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6521.5585
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3262929
X-RAY DIFFRACTIONr_scbond_it2.1433442
X-RAY DIFFRACTIONr_scangle_it3.5474.5453
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.399→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 121 -
Rwork0.239 2246 -
obs--99 %

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