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- PDB-3u50: Crystal Structure of the Tetrahymena telomerase processivity fact... -

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Basic information

Entry
Database: PDB / ID: 3u50
TitleCrystal Structure of the Tetrahymena telomerase processivity factor Teb1 OB-C
ComponentsTelomerase-associated protein 82
KeywordsDNA BINDING PROTEIN / tetrahymena / telomerase / Teb1 / processivity factor
Function / homology
Function and homology information


single-stranded telomeric DNA binding / telomerase holoenzyme complex / telomere maintenance via telomerase / chromosome, telomeric region / zinc ion binding
Similarity search - Function
: / Replication factor A, C-terminal / Replication factor-A C terminal domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Single Sheet / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Telomeric repeat-binding subunit 1
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsZeng, Z. / Huang, J. / Yang, Y. / Lei, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for Tetrahymena telomerase processivity factor Teb1 binding to single-stranded telomeric-repeat DNA.
Authors: Zeng, Z. / Min, B. / Huang, J. / Hong, K. / Yang, Y. / Collins, K. / Lei, M.
History
DepositionOct 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Jan 28, 2015Group: Other
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Telomerase-associated protein 82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3482
Polymers20,2831
Non-polymers651
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.609, 80.609, 82.081
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Telomerase-associated protein 82


Mass: 20283.000 Da / Num. of mol.: 1 / Fragment: unp residues 511-682
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Gene: TAP82 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D2CVN6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.8 Å3/Da / Density % sol: 67.59 %
Crystal growTemperature: 277 K / pH: 5.2
Details: 3.8 M NaCl, pH 5.2, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9787
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 10822 / % possible obs: 97.9 % / Redundancy: 10 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.357 / % possible all: 82.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.5→36.18 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 1.35 / Phase error: 27.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 1110 10.29 %
Rwork0.214 --
obs0.218 10792 97.8 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.59 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 58.76 Å2
Baniso -1Baniso -2Baniso -3
1-5.7335 Å2-0 Å2-0 Å2
2--5.7335 Å20 Å2
3----11.4669 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 1 18 1356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091361
X-RAY DIFFRACTIONf_angle_d1.1391826
X-RAY DIFFRACTIONf_dihedral_angle_d17.87517
X-RAY DIFFRACTIONf_chiral_restr0.082195
X-RAY DIFFRACTIONf_plane_restr0.005237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.61380.39031160.30761035X-RAY DIFFRACTION85
2.6138-2.75160.35651360.30031189X-RAY DIFFRACTION99
2.7516-2.92390.37461350.29051224X-RAY DIFFRACTION100
2.9239-3.14950.31941350.26511211X-RAY DIFFRACTION100
3.1495-3.46620.29681430.23411234X-RAY DIFFRACTION100
3.4662-3.96730.23341520.20151234X-RAY DIFFRACTION100
3.9673-4.99630.19081400.16141249X-RAY DIFFRACTION100
4.9963-36.1820.22371530.21306X-RAY DIFFRACTION100

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