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- PDB-5npt: Structure of the N-terminal domain of the yeast telomerase revers... -

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Basic information

Entry
Database: PDB / ID: 5npt
TitleStructure of the N-terminal domain of the yeast telomerase reverse transcriptase
ComponentsTelomerase reverse transcriptase
KeywordsTRANSCRIPTION / telomerase
Function / homology
Function and homology information


: / RNA-directed DNA polymerase / chromosome, telomeric region / DNA binding / nucleus / metal ion binding
Similarity search - Function
Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Telomerase reverse transcriptase
Similarity search - Component
Biological speciesOgataea polymorpha (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRodina, E.V. / Lebedev, A.A. / Hakanpaa, J. / Hackenberg, C. / Petrova, O.A. / Zvereva, M.I. / Dontsova, O.A. / Lamzin, V.S.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structure and function of the N-terminal domain of the yeast telomerase reverse transcriptase.
Authors: Petrova, O.A. / Mantsyzov, A.B. / Rodina, E.V. / Efimov, S.V. / Hackenberg, C. / Hakanpaa, J. / Klochkov, V.V. / Lebedev, A.A. / Chugunova, A.A. / Malyavko, A.N. / Zatsepin, T.S. / Mishin, A. ...Authors: Petrova, O.A. / Mantsyzov, A.B. / Rodina, E.V. / Efimov, S.V. / Hackenberg, C. / Hakanpaa, J. / Klochkov, V.V. / Lebedev, A.A. / Chugunova, A.A. / Malyavko, A.N. / Zatsepin, T.S. / Mishin, A.V. / Zvereva, M.I. / Lamzin, V.S. / Dontsova, O.A. / Polshakov, V.I.
History
DepositionApr 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomerase reverse transcriptase


Theoretical massNumber of molelcules
Total (without water)18,5851
Polymers18,5851
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.195, 64.098, 126.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Telomerase reverse transcriptase


Mass: 18584.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ogataea polymorpha (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R4IT35
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ELECTRON DENSITY MAP CONTAINS MANY BLOBS AND CONTINUOUS NON-INTERPRETABLE PATCHES OF DENSITY, ...THE ELECTRON DENSITY MAP CONTAINS MANY BLOBS AND CONTINUOUS NON-INTERPRETABLE PATCHES OF DENSITY, POSSIBLY OWING TO DISORDERED REGIONS INCLUDING SHORT POLYPEPTIDES PRODUCED DURING CRYSTALLISATION UNDER PROTEOLYTIC CONDITIONS. IN PARTICULAR, THE DENSITY IN THE REGION BETWEEN TRP28 AND GLU34 COULD NOT BE INTERPRETED IN TERMS OF ATOMIC MODEL BUT HAS FEATURES SUGGESTING THE PRESENCE OF CHAIN FRAGMENTS CLEAVED AT ARG33 AND OVERLAPPING WITH THEMSELVES AND, POSSIBLY, WITH THE COMPONENTS OF CRYSTALLIZATION SOLUTION. SIMILARLY, A WEAK BUT CONTINUOUS ELECTRON DENSITY BEYOND VAL81 AND LEU141 COULD NOT BE RELIABLY INTERPRETED.

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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: 2.08 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 10.5
Details: Sodium-potassium-phosphate, sodium citrate and CAPS buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97858 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97858 Å / Relative weight: 1
ReflectionResolution: 2.4→63.03 Å / Num. obs: 6202 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 54.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.029 / Net I/σ(I): 20.6
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.347 / Num. unique obs: 3177 / CC1/2: 0.971 / Rpim(I) all: 0.194 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INCOMPLETE MODEL OF SE-MET VARIANT SOLVED BY SAD METHOD USING CRANK2 SOFTWARE

Resolution: 2.4→63.03 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 16.623 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22364 298 4.8 %RANDOM
Rwork0.18623 ---
obs0.18806 5904 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.192 Å2
Baniso -1Baniso -2Baniso -3
1--2.53 Å20 Å20 Å2
2--0.26 Å20 Å2
3---2.28 Å2
Refinement stepCycle: 1 / Resolution: 2.4→63.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1017 0 0 6 1023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191038
X-RAY DIFFRACTIONr_bond_other_d0.0020.02977
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9571409
X-RAY DIFFRACTIONr_angle_other_deg1.03832236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5015122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.15324.31451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60115179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.129156
X-RAY DIFFRACTIONr_chiral_restr0.0980.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021157
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02239
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5174.742497
X-RAY DIFFRACTIONr_mcbond_other2.5144.749498
X-RAY DIFFRACTIONr_mcangle_it3.9867.091618
X-RAY DIFFRACTIONr_mcangle_other3.9857.092618
X-RAY DIFFRACTIONr_scbond_it3.0045.09541
X-RAY DIFFRACTIONr_scbond_other3.0015.095542
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7747.503791
X-RAY DIFFRACTIONr_long_range_B_refined6.58253.7751152
X-RAY DIFFRACTIONr_long_range_B_other6.58453.8331153
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 26 -
Rwork0.216 422 -
obs--98.25 %
Refinement TLS params.Method: refined / Origin x: 10.198 Å / Origin y: 3.492 Å / Origin z: 15.363 Å
111213212223313233
T0.1933 Å2-0.0312 Å20.0114 Å2-0.0739 Å20.0127 Å2--0.0045 Å2
L0.9165 °20.8122 °20.2792 °2-3.2563 °2-0.0119 °2--6.2641 °2
S0.0093 Å °-0.0381 Å °-0.0127 Å °-0.2402 Å °0.0331 Å °-0.0321 Å °0.5565 Å °-0.1672 Å °-0.0424 Å °

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