- PDB-2wc9: Crystal structure of the g2p (large terminase) nuclease domain fr... -
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Basic information
Entry
Database: PDB / ID: 2wc9
Title
Crystal structure of the g2p (large terminase) nuclease domain from the bacteriophage SPP1 with bound Mn
Components
TERMINASE LARGE SUBUNIT
Keywords
VIRAL PROTEIN / DNA TRANSLOCATION
Function / homology
Function and homology information
viral terminase, large subunit / viral DNA genome packaging / nuclease activity / chromosome organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / ATP binding / metal ion binding Similarity search - Function
Phage terminase large subunit, C-terminal / Terminase, large subunit SPP1-like / Nucleotidyltransferase; domain 5 - #280 / Terminase RNAseH like domain / Phage terminase large subunit, N-terminal / Phage terminase large subunit / Bacteriophage terminase, large subunit / Nucleotidyltransferase; domain 5 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 2.5→60.4 Å / Num. obs: 7520 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 32.4
Reflection shell
Resolution: 2.5→2.64 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.4 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.5.0082
refinement
MOSFLM
datareduction
SCALA
datascaling
Refinement
Method to determine structure: OTHER Starting model: NONE Resolution: 2.5→24.6 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 21.218 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.546 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25862
349
4.7 %
RANDOM
Rwork
0.19502
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obs
0.19781
7142
100 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK