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- PDB-2b2a: Crystal Structure of the TEN domain of the Telomerase Reverse Tra... -

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Basic information

Entry
Database: PDB / ID: 2b2a
TitleCrystal Structure of the TEN domain of the Telomerase Reverse Transcriptase
ComponentsTelomerase reverse transcriptase
KeywordsTRANSFERASE / Telomerase / TERT / Reverse Transcriptase / RT
Function / homology
Function and homology information


telomerase catalytic core complex / telomerase activity / telomerase holoenzyme complex / telomerase RNA binding / telomeric DNA binding / telomere maintenance via telomerase / RNA-directed DNA polymerase / chromosome, telomeric region / metal ion binding
Similarity search - Function
: / Telomerase reverse transcriptase, TEN domain / Telomerase reverse transcriptase, CTE domain / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile.
Similarity search - Domain/homology
Telomerase reverse transcriptase
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.22 Å
AuthorsJacobs, S.A. / Podell, E.R. / Cech, T.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Crystal structure of the essential N-terminal domain of telomerase reverse transcriptase.
Authors: Jacobs, S.A. / Podell, E.R. / Cech, T.R.
History
DepositionSep 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomerase reverse transcriptase
B: Telomerase reverse transcriptase
C: Telomerase reverse transcriptase


Theoretical massNumber of molelcules
Total (without water)70,8653
Polymers70,8653
Non-polymers00
Water1,72996
1
A: Telomerase reverse transcriptase


Theoretical massNumber of molelcules
Total (without water)23,6221
Polymers23,6221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Telomerase reverse transcriptase


Theoretical massNumber of molelcules
Total (without water)23,6221
Polymers23,6221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Telomerase reverse transcriptase


Theoretical massNumber of molelcules
Total (without water)23,6221
Polymers23,6221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.100, 111.100, 42.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Telomerase reverse transcriptase / Telomerase catalytic subunit / Telomerase subunit P133


Mass: 23621.818 Da / Num. of mol.: 3 / Fragment: TEN domain / Mutation: L87M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Gene: TERT / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O77448, RNA-directed DNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 2000 MMe, Magnesium Nitrate hexahydrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.000, 0.953725, 0.97957, 0.97976
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 17, 2005
RadiationMonochromator: Double crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9537251
30.979571
40.979761
ReflectionResolution: 2.22→500 Å / Num. all: 28712 / Num. obs: 28712 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 15.5
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 4.55 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2811 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.22→19.71 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 123680.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2711 9.9 %RANDOM
Rwork0.238 ---
all0.238 27290 --
obs0.238 27290 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.0637 Å2 / ksol: 0.345341 e/Å3
Displacement parametersBiso mean: 37.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.91 Å26.04 Å20 Å2
2--3.91 Å20 Å2
3----7.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.22→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 0 96 4048
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_mcangle_it2.72
X-RAY DIFFRACTIONc_scbond_it2.222
X-RAY DIFFRACTIONc_scangle_it3.462.5
LS refinement shellResolution: 2.22→2.36 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 417 10.1 %
Rwork0.307 3712 -
obs-3712 86.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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