+Open data
-Basic information
Entry | Database: PDB / ID: 5k5d | ||||||
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Title | Structure of the C2221 form of Pnob8-like ParB-N domain | ||||||
Components | ParB domain protein nuclease | ||||||
Keywords | HYDROLASE / ParB-N / pnob8 / partition | ||||||
Function / homology | ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / CITRIC ACID / ParB domain protein nuclease Function and homology information | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 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-Castneda, 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 | 5k5d.cif.gz | 170.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k5d.ent.gz | 135.9 KB | Display | PDB format |
PDBx/mmJSON format | 5k5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/5k5d ftp://data.pdbj.org/pub/pdb/validation_reports/k5/5k5d | HTTPS FTP |
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-Related structure data
Related structure data | 4rs7C 4rs8C 5k5aSC 5k5oC 5k5qC 5k5rC 5k5zC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 35508.680 Da / Num. of mol.: 3 / Fragment: UNP residues 1-298 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 #2: Chemical | ChemComp-CIT / #3: Water | ChemComp-HOH / | Sequence details | protein had degraded within its C-terminal domain during crystallization | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 56.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, |
-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: Dec 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→46.107 Å / Num. obs: 38446 / % possible obs: 95.57 % / Redundancy: 4.3 % / Rsym value: 0.08 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.39 / % possible all: 83.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5K5A Resolution: 2.45→46.107 Å / FOM work R set: 0.8177 / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.835 Å2 / ksol: 0.396 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 265.11 Å2 / Biso mean: 60.69 Å2 / Biso min: 18.18 Å2
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Refinement step | Cycle: final / Resolution: 2.45→46.107 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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