|Entry||Database: PDB / ID: 6h8o|
|Title||Crystal structure of the Master-Rep protein nuclease domain from the Faba Bean Necrotic Yellows Virus|
|Keywords||REPLICATION / endonuclease / Faba Bean Necrotic Yellows Virus / Rep protein / DNA replication|
|Function / homology|
Function and homology information
protein-DNA covalent cross-linking / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA helicase activity / DNA replication / host cell nucleus / ATP hydrolysis activity ...protein-DNA covalent cross-linking / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA helicase activity / DNA replication / host cell nucleus / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Viral replication-associated protein, N-terminal / Putative viral replication protein / Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Replication-associated protein / Master replication protein
Similarity search - Component
|Biological species||Faba bean necrotic yellows virus|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å|
|Authors||Moncalian, G. / Gonzalez-Montes, L.|
|Funding support|| Spain, 1items |
|Citation||Journal: To Be Published|
Title: Crystal structure of the Master-Rep protein nuclease domain from the Faba Bean Necrotic Yellows Virus
Authors: Moncalian, G. / Gonzalez-Montes, L.
|Structure viewer||Molecule: |
Downloads & links
A: Replication-associated protein
B: Replication-associated protein
A: Replication-associated protein
B: Replication-associated protein
Mass: 10954.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Faba bean necrotic yellows virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2D0XNJ4, UniProt: O39828*PLUS
|#3: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.67 Å3/Da / Density % sol: 53.9 %|
|Crystal grow||Temperature: 295 K / Method: vapor diffusion, sitting drop|
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium citrate tribasis dihydrate pH5.6, 2.0 M Ammonium sulfate
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.99989 Å|
|Detector||Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2016|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.99989 Å / Relative weight: 1|
|Reflection||Resolution: 1.15→47.115 Å / Num. obs: 81485 / % possible obs: 99.4 % / Redundancy: 15.4 % / Biso Wilson estimate: 11.36 Å2 / CC1/2: 0.997 / Net I/σ(I): 19.5|
|Reflection shell||Resolution: 1.15→1.21 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 5.6 / Num. unique obs: 11361 / CC1/2: 0.944 / % possible all: 95.6|
|Refinement||Method to determine structure: SAD|
Starting model: I3C
Resolution: 1.15→47.115 Å / Cross valid method: FREE R-VALUE
|Refinement step||Cycle: LAST / Resolution: 1.15→47.115 Å|
|LS refinement shell||Resolution: 1.15→1.191 Å|
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