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- PDB-4dyc: Crystal Structure of the terminase small subunit gp1 with D19R mu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dyc | ||||||
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Title | Crystal Structure of the terminase small subunit gp1 with D19R mutation of the bacterial virus sf6 | ||||||
![]() | Terminase small subunit | ||||||
![]() | VIRAL PROTEIN / gp1 / DNA-binding | ||||||
Function / homology | Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / Terminase small subunit![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhao, H. / Tang, L. | ||||||
![]() | ![]() Title: Structural and Functional Studies of the Phage Sf6 Terminase Small Subunit Reveal a DNA-Spooling Device Facilitated by Structural Plasticity. Authors: Zhao, H. / Kamau, Y.N. / Christensen, T.E. / Tang, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.2 KB | Display | ![]() |
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PDB format | ![]() | 48.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.9 KB | Display | ![]() |
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Full document | ![]() | 435.9 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 19 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dyqC ![]() 4dyrC ![]() 4dzjC ![]() 4dzpC ![]() 3hefS 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15576.782 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.4 Details: 1.2M NAH2PO4/0.8M K2HPO4, 0.2M LI2SO4, pH 6.4, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2010 |
Radiation | Monochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 27710 / Num. obs: 27608 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.57 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 30.61 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 13.03 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 4.45 / Num. unique all: 1938 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3HEF Resolution: 1.8→19.805 Å / SU ML: 0.02 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 4.45 / Phase error: 22.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.089 Å2 / ksol: 0.385 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.805 Å
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Refine LS restraints |
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LS refinement shell |
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