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- PDB-7nlh: S. cerevisiae Ty1 p22 restriction factor, Gag CA-CTD, AUG1 variant -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nlh | ||||||||||||
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Title | S. cerevisiae Ty1 p22 restriction factor, Gag CA-CTD, AUG1 variant | ||||||||||||
![]() | Ty1 Gag p22 | ||||||||||||
![]() | VIRUS LIKE PARTICLE / Restriction factor / Ty1 / Gag / CA | ||||||||||||
Function / homology | Ty transposon capsid protein / Ty transposon capsid protein / RNA binding / cytoplasm / Transposon TyH3 Gag polyprotein![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Cottee, M.A. / Taylor, I.A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of a Ty1 restriction factor reveals the molecular basis of transposition copy number control. Authors: Cottee, M.A. / Beckwith, S.L. / Letham, S.C. / Kim, S.J. / Young, G.R. / Stoye, J.P. / Garfinkel, D.J. / Taylor, I.A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.9 KB | Display | ![]() |
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PDB format | ![]() | 99.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.1 KB | Display | ![]() |
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Full document | ![]() | 449.9 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 14.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 13452.185 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S288C / Gene: TY1A, GAG, TYA1 / Plasmid: pET22b / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.07 Å3/Da / Density % sol: 79.76 % / Description: 160x160x160 hexagonal prism |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 300 nl protein (6.25 mg mL-1, in 20 mM Tris-HCl pH 8.5, 150 mM NaCl, 1 mM TCEP) 100 nl Mother Liquor (1.16 M Li2SO4, 0.1 M Tris-HCl pH 9.0) pH screened 7.5-9.0, Li2SO4 screened 1.125M-1.25M. PH range: 7.5-9.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97954 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→244.4 Å / Num. obs: 23876 / % possible obs: 100 % / Redundancy: 38.7 % / CC1/2: 1 / Rpim(I) all: 0.016 / Rrim(I) all: 0.101 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 38.6 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3390 / CC1/2: 0.491 / Rpim(I) all: 0.627 / Rrim(I) all: 3.912 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Ty1 p22 Aug2 variant partial model Resolution: 2.8→141.46 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.928 / SU B: 32.897 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 266.65 Å2 / Biso mean: 145.564 Å2 / Biso min: 94.58 Å2
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Refinement step | Cycle: final / Resolution: 2.8→141.46 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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