+Open data
-Basic information
Entry | Database: PDB / ID: 6zd1 | ||||||
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Title | Structure of apo telomerase from Candida Tropicalis | ||||||
Components | Telomerase reverse transcriptase | ||||||
Keywords | REPLICATION / Telomerase / catalytic core / RNA binding / telomere | ||||||
Function / homology | Function and homology information telomerase catalytic core complex / telomerase RNA reverse transcriptase activity / telomerase RNA binding / telomeric DNA binding / telomere maintenance via telomerase / RNA-directed DNA polymerase / chromosome, telomeric region / metal ion binding Similarity search - Function | ||||||
Biological species | Candida tropicalis MYA-3404 (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.47 Å | ||||||
Authors | Zhai, L. / Rety, S. / Chen, W.F. / Auguin, D. / Xi, X.G. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Crystal structures of N-terminally truncated telomerase reverse transcriptase from fungi‡. Authors: Zhai, L.T. / Rety, S. / Chen, W.F. / Song, Z.Y. / Auguin, D. / Sun, B. / Dou, S.X. / 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 | 6zd1.cif.gz | 312.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zd1.ent.gz | 235.1 KB | Display | PDB format |
PDBx/mmJSON format | 6zd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/6zd1 ftp://data.pdbj.org/pub/pdb/validation_reports/zd/6zd1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 82380.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida tropicalis MYA-3404 (yeast) / Gene: CTRG_04008 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: C5MCQ7, RNA-directed DNA polymerase |
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#2: 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: 2.56 Å3/Da / Density % sol: 51.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.1 Details: 0.2 M sodium citrate tribasic dihydrate 0.1 M Bis-Tris propane (pH 6.1) 15% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.467→43.78 Å / Num. obs: 54095 / % possible obs: 85.11 % / Redundancy: 6.8 % / Biso Wilson estimate: 67.8 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1502 / Rpim(I) all: 0.0617 / Rrim(I) all: 0.1626 / Net I/σ(I): 10.47 |
Reflection shell | Resolution: 2.467→2.555 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.652 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 996 / CC1/2: 0.543 / CC star: 0.624 / Rpim(I) all: 0.507 / Rrim(I) all: 1.804 / % possible all: 45.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.47→43.78 Å / SU ML: 0.348 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.0246 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: 82.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.47→43.78 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 / Auth asym-ID: A / Label asym-ID: A
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