+Open data
-Basic information
Entry | Database: PDB / ID: 6zd6 | ||||||
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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 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 / MOLECULAR REPLACEMENT / Resolution: 2.64 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 | 6zd6.cif.gz | 340.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zd6.ent.gz | 234.4 KB | Display | PDB format |
PDBx/mmJSON format | 6zd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/6zd6 ftp://data.pdbj.org/pub/pdb/validation_reports/zd/6zd6 | HTTPS FTP |
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-Related structure data
Related structure data | 6zd1SC 6zd2C 6zdpC 6zdqC 6zduC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 81779.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: mutation R366C and S774C / 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 / |
-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: 51.9 % |
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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: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980109 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980109 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→64.77 Å / Num. obs: 47515 / % possible obs: 83.19 % / Redundancy: 14.5 % / Biso Wilson estimate: 87.42 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1768 / Rpim(I) all: 0.04795 / Rrim(I) all: 0.1832 / Net I/σ(I): 10.99 |
Reflection shell | Resolution: 2.642→2.736 Å / Redundancy: 14.8 % / Rmerge(I) obs: 2.347 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 225 / CC1/2: 0.575 / Rpim(I) all: 0.635 / Rrim(I) all: 2.432 / % possible all: 48.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ZD1 Resolution: 2.64→64.77 Å / SU ML: 0.388 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.2104 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: 105.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.64→64.77 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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