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- PDB-5nxh: Crystal structure of the carboxy-terminal region of the bacteriop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nxh | ||||||
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Title | Crystal structure of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34, residues 744-1289 at 2.9 Angstrom resolution | ||||||
![]() | Long-tail fiber proximal subunit | ||||||
![]() | VIRAL PROTEIN / CAUDOVIRALES / MYOVIRIDAE / STRUCTURAL PROTEIN | ||||||
Function / homology | : / : / Long-tail fiber proximal subunit, C-terminal, trimerization domain / Long-tail fiber proximal subunit, C-terminal, second / virus tail, fiber / Long-tail fiber proximal subunit![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Namura, M. / van Raaij, M.J. / Kanamaru, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of the Carboxy-Terminal Region of the Bacteriophage T4 Proximal Long Tail Fiber Protein Gp34. Authors: Granell, M. / Namura, M. / Alvira, S. / Kanamaru, S. / van Raaij, M.J. #1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014 Title: Crystallization of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34. Authors: Granell, M. / Namura, M. / Alvira, S. / Garcia-Doval, C. / Singh, A.K. / Gutsche, I. / van Raaij, M.J. / Kanamaru, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 321.5 KB | Display | ![]() |
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PDB format | ![]() | 260 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.2 KB | Display | ![]() |
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Full document | ![]() | 477.2 KB | Display | |
Data in XML | ![]() | 59.3 KB | Display | |
Data in CIF | ![]() | 82.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4uxeC ![]() 4uxfC ![]() 4uxgC ![]() 5nxfSC S: Starting model for refinement C: citing same article ( |
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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: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 744 - 1289 / Label seq-ID: 19 - 564
NCS ensembles :
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Components
#1: Protein | Mass: 60815.098 Da / Num. of mol.: 3 / Fragment: UNP residue 726-1289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.43 % / Description: Semi-ellipsoidal-shaped plates |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 4-7% (w/v) PEG 6000 100 mM Tris-HCl pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→45.18 Å / Num. obs: 48930 / % possible obs: 96.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 69.5 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.89→3.04 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 3 / Num. unique obs: 6784 / % possible all: 91.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5NXF Resolution: 2.89→45.18 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.894 / SU B: 20.699 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / 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: 64.78 Å2
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Refinement step | Cycle: 1 / Resolution: 2.89→45.18 Å
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Refine LS restraints |
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