+Open data
-Basic information
Entry | Database: PDB / ID: 5k5a | |||||||||
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Title | Structure of the pNOB8-like ParB N-domain | |||||||||
Components | ParB domain protein nuclease | |||||||||
Keywords | HYDROLASE / ParB / pNOB8 / partition / DNA segregation / archaea | |||||||||
Function / homology | ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / ParB domain protein nuclease Function and homology information | |||||||||
Biological species | Sulfolobus solfataricus (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.825 Å | |||||||||
Authors | Schumacher, M. | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k5a.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k5a.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 5k5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/5k5a ftp://data.pdbj.org/pub/pdb/validation_reports/k5/5k5a | HTTPS FTP |
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-Related structure data
Related structure data | 4rs7C 4rs8C 5k5dC 5k5oC 5k5qC 5k5rC 5k5zC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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Sequence details | protein had degraded within its C-terminal domain during crystallization. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Highest resolution: 2.825 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Bsol: 71.694 Å2 / ksol: 0.319 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 194.03 Å2 / Biso mean: 106.99 Å2 / Biso min: 42.19 Å2
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Refinement step | Cycle: final / Resolution: 2.825→58.371 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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