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- PDB-3ezk: Bacteriophage T4 gp17 motor assembly based on crystal structures ... -

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Basic information

Entry
Database: PDB / ID: 3ezk
TitleBacteriophage T4 gp17 motor assembly based on crystal structures and cryo-EM reconstructions
DescriptorDNA packaging protein Gp17
KeywordsHYDROLASE / pentameric motor / DNA packaging / Alternative initiation / ATP-binding / DNA-binding / Hydrolase / Nuclease / Nucleotide-binding
Specimen sourceBacteriophage T4 / virus
MethodElectron microscopy (34 Å resolution / Particle / Single particle)
AuthorsSun, S. / Rossmann, M.G.
CitationCell, 2008, 135, 1251-1262

Cell, 2008, 135, 1251-1262 Yorodumi Papers
The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces.
Siyang Sun / Kiran Kondabagil / Bonnie Draper / Tanfis I Alam / Valorie D Bowman / Zhihong Zhang / Shylaja Hegde / Andrei Fokine / Michael G Rossmann / Venigalla B Rao

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 23, 2008 / Release: Jan 13, 2009
RevisionDateData content typeGroupProviderType
1.0Jan 13, 2009Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

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Assembly

Deposited unit
A: DNA packaging protein Gp17
B: DNA packaging protein Gp17
C: DNA packaging protein Gp17
D: DNA packaging protein Gp17
E: DNA packaging protein Gp17


Theoretical massNumber of molelcules
Total (without water)331,0205
Polyers331,0205
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)
DNA packaging protein Gp17 / Terminase / Coordinate model: Cα atoms only


Mass: 66204.062 Da / Num. of mol.: 5 / Fragment: Residues 1-577 / Source: (gene. exp.) Bacteriophage T4 / virus / References: UniProt: P17312

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: T4 procapsid with gp17 bound / Type: VIRUS
Buffer solutionName: 50mM Tris-HCl, 100mM NaCl, 5mM MgCl2, 3mM beta-Mercaptoethanol
Details: 50mM Tris-HCl, 100mM NaCl, 5mM MgCl2, 3mM beta-Mercaptoethanol
pH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: flash-frozen on holey grids in liquid ethane

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 38000 / Nominal defocus max: 3500 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1EMFitMODEL FITTING
2SPIDERRECONSTRUCTION
CTF correctionDetails: phase flipping of each micrograph
SymmetryPoint symmetry: C5
3D reconstructionMethod: Spider / Resolution: 34 Å / Number of particles: 1716 / Nominal pixel size: 6.48 / Actual pixel size: 6.48 / Symmetry type: POINT
Atomic model buildingDetails: METHOD--N- and C-terminal domains were separately fitted into their corresponding cryoEM densities REFINEMENT PROTOCOL--Rigid body
Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Sumf
Atomic model buildingPDB-ID: 3CPE
Number of atoms included #LASTProtein: 2765 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2765

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