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Yorodumi- PDB-8bh9: Structure of Est1 from Candida Tropicalis in complex with TLC1 te... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bh9 | ||||||
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Title | Structure of Est1 from Candida Tropicalis in complex with TLC1 telomerase RNA fragment 427-435 / 496-504 | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / Telomerase TLC1 RNA | ||||||
Function / homology | Function and homology information Est1/Ebs1-like / Telomerase activating protein Est1-like, N-terminal / Telomerase activating protein Est1 / DNA/RNA-binding domain, Est1-type / Est1 DNA/RNA binding domain / Tetratricopeptide-like helical domain superfamily Similarity search - Domain/homology | ||||||
Biological species | Candida tropicalis MYA-3404 (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å | ||||||
Authors | Rety, S. / Chen, W.F. / Xi, X.G. | ||||||
Funding support | France, 1items
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Citation | Journal: To Be Published Title: Structure of Est1 from Candida Tropicalis in complex with TLC1 telomerase RNA fragment 427-435 / 496-504 Authors: Rety, S. / Chen, W.F. / Xi, X.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bh9.cif.gz | 299.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bh9.ent.gz | 200.4 KB | Display | PDB format |
PDBx/mmJSON format | 8bh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/8bh9 ftp://data.pdbj.org/pub/pdb/validation_reports/bh/8bh9 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 62701.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida tropicalis MYA-3404 (yeast) / Strain: ATCC MYA-3404 / T1 / Gene: CTRG_06152 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: C5MJA9 | ||||
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#2: RNA chain | Mass: 3820.344 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: TLC1 RNA fragment 427-435/ 496-504 with 436-495 deletion Source: (synth.) Candida tropicalis MYA-3404 (yeast) | ||||
#3: Chemical | ChemComp-K / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 4K 20% PEG 200 5% Tris-HCl 0.1M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97888 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97888 Å / Relative weight: 1 |
Reflection | Resolution: 2.086→109.126 Å / Num. obs: 37916 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 42.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.086→2.122 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.927 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1910 / CC1/2: 0.834 / Rpim(I) all: 0.366 / Rrim(I) all: 0.998 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.09→34.87 Å / SU ML: 0.2252 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.7187 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→34.87 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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