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- PDB-4bls: P4 PROTEIN FROM BACTERIOPHAGE PHI12 Q278A MUTANT IN COMPLEX WITH ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bls | ||||||
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Title | P4 PROTEIN FROM BACTERIOPHAGE PHI12 Q278A MUTANT IN COMPLEX WITH AMPcPP | ||||||
![]() | NTPASE P4 | ||||||
![]() | HYDROLASE / PACKAGING / CYSTOVIRIDAE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | El Omari, K. / Meier, C. / Kainov, D. / Sutton, G. / Grimes, J.M. / Poranen, M.M. / Bamford, D.H. / Tuma, R. / Stuart, D.I. / Mancini, E.J. | ||||||
![]() | ![]() Title: Tracking in atomic detail the functional specializations in viral RecA helicases that occur during evolution. Authors: Kamel El Omari / Christoph Meier / Denis Kainov / Geoff Sutton / Jonathan M Grimes / Minna M Poranen / Dennis H Bamford / Roman Tuma / David I Stuart / Erika J Mancini / ![]() Abstract: Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, ...Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, uses chemical energy to translocate single-stranded RNA genomic precursors into the procapsid. We previously dissected the mechanism of RNA translocation for one such phage, 12, and have now investigated three further highly divergent, cystoviral P4 NTPases (from 6, 8 and 13). High-resolution crystal structures of the set of P4s allow a structure-based phylogenetic analysis, which reveals that these proteins form a distinct subfamily of the RecA-type ATPases. Although the proteins share a common catalytic core, they have different specificities and control mechanisms, which we map onto divergent N- and C-terminal domains. Thus, the RNA loading and tight coupling of NTPase activity with RNA translocation in 8 P4 is due to a remarkable C-terminal structure, which wraps right around the outside of the molecule to insert into the central hole where RNA binds to coupled L1 and L2 loops, whereas in 12 P4, a C-terminal residue, serine 282, forms a specific hydrogen bond to the N7 of purines ring to confer purine specificity for the 12 enzyme. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 349 KB | Display | ![]() |
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PDB format | ![]() | 286.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4bloC ![]() 4blpC ![]() 4blqC ![]() 4blrC ![]() 4bltC ![]() 4bwyC ![]() 1w44S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 35093.379 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | pH: 4.8 Details: 10% PEG 1500 IN 100 MM SODIUM ACETATE PH 4.8, AND 5MM AMCPP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9756 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 32832 / % possible obs: 94.6 % / Observed criterion σ(I): 7.1 / Redundancy: 6.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 7.1 / % possible all: 93.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1W44 Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.911 / SU B: 28.229 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R: 1.167 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.169 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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