+Open data
-Basic information
Entry | Database: PDB / ID: 6k9b | ||||||
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Title | Apo structure of NrS-1 N terminal domain N305 | ||||||
Components | Primase | ||||||
Keywords | TRANSFERASE / primase / polymerase | ||||||
Function / homology | Function and homology information viral DNA genome replication / helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / DNA helicase / DNA replication / DNA-directed DNA polymerase / hydrolase activity / ATP binding Similarity search - Function | ||||||
Biological species | Nitratiruptor phage NrS-1 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Chen, X. / Gan, J. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structural studies reveal a unique ring-shaped helicase architecture at the C-terminus of deep-sea vent phage DNA polymerase Authors: Chen, X. / Gan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k9b.cif.gz | 121.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k9b.ent.gz | 94.4 KB | Display | PDB format |
PDBx/mmJSON format | 6k9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/6k9b ftp://data.pdbj.org/pub/pdb/validation_reports/k9/6k9b | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 0 / Auth seq-ID: 0 - 292 / Label seq-ID: 1 - 293
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-Components
#1: Protein | Mass: 34862.238 Da / Num. of mol.: 2 / Fragment: N terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitratiruptor phage NrS-1 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M5AAG8 #2: Water | ChemComp-HOH / | |
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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: 2.52 Å3/Da / Density % sol: 51.12 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Bis-tris pH 6.5, 25% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å | |||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2018 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.45→30 Å / Num. obs: 24723 / % possible obs: 97.1 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.134 / Net I/σ(I): 10.2 | |||||||||||||||
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2338 / Rrim(I) all: 0.438 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→29.52 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.896 / SU B: 6.288 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.058 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.29 Å2
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Refinement step | Cycle: 1 / Resolution: 2.45→29.52 Å
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Refine LS restraints |
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