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- PDB-5k5a: Structure of the pNOB8-like ParB N-domain -

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Basic information

Entry
Database: PDB / ID: 5k5a
TitleStructure of the pNOB8-like ParB N-domain
ComponentsParB domain protein nuclease
KeywordsHYDROLASE / ParB / pNOB8 / partition / DNA segregation / archaea
Function / homology: / Ssol_1539-like, second domain / ParB N-terminal domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / ParB domain protein nuclease
Function and homology information
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.825 Å
AuthorsSchumacher, M.
CitationJournal: Science / Year: 2015
Title: Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages.
Authors: Schumacher, M.A. / Tonthat, N.K. / Lee, J. / Rodriguez-Castaneda, F.A. / Chinnam, N.B. / Kalliomaa-Sanford, A.K. / Ng, I.W. / Barge, M.T. / Shaw, P.L. / Barilla, D.
History
DepositionMay 23, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionJun 15, 2016ID: 4RSF
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: ParB domain protein nuclease


Theoretical massNumber of molelcules
Total (without water)35,2491
Polymers35,2491
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)102.400, 62.000, 62.000
Angle α, β, γ (deg.)90.000, 109.700, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ParB domain protein nuclease


Mass: 35248.953 Da / Num. of mol.: 1 / Fragment: UNP residues 2-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: 98/2 / Gene: Ssol_1539 / Production host: Escherichia coli (E. coli) / References: UniProt: D0KSP7
Has protein modificationY
Sequence detailsprotein had degraded within its C-terminal domain during crystallization.

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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: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, citrate

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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 315r / Detector: CCD / Date: Nov 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.825→58.371 Å / Num. obs: 17036 / % possible obs: 99.09 % / Redundancy: 3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9
Reflection shellHighest resolution: 2.825 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.825→58.371 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 32.65
RfactorNum. reflection% reflection
Rfree0.2762 883 9.95 %
Rwork0.2319 --
obs0.2363 17036 99.09 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Bsol: 71.694 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 194.03 Å2 / Biso mean: 106.99 Å2 / Biso min: 42.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.0727 Å2-0 Å2-4.4401 Å2
2---8.551 Å2-0 Å2
3---8.6237 Å2
Refinement stepCycle: final / Resolution: 2.825→58.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 0 0 2210
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032265
X-RAY DIFFRACTIONf_angle_d0.5323036
X-RAY DIFFRACTIONf_chiral_restr0.037346
X-RAY DIFFRACTIONf_plane_restr0.002386
X-RAY DIFFRACTIONf_dihedral_angle_d14.361903
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8254-2.92640.39981630.37331493165697
2.9264-3.04350.38971670.348715271694100
3.0435-3.1820.40691740.329815491723100
3.182-3.34980.331690.279715541723100
3.3498-3.55960.36351700.278615481718100
3.5596-3.83440.29281740.246615501724100
3.8344-4.22020.32631710.219815461717100
4.2202-4.83060.24121720.18815301702100
4.8306-6.0850.30991640.24261511167597
6.085-58.38360.18751710.19411533170499

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