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- PDB-1otc: THE O. NOVA TELOMERE END BINDING PROTEIN COMPLEXED WITH SINGLE ST... -

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Basic information

Entry
Database: PDB / ID: 1otc
TitleTHE O. NOVA TELOMERE END BINDING PROTEIN COMPLEXED WITH SINGLE STRAND DNA
Components
  • DNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')
  • PROTEIN (TELOMERE-BINDING PROTEIN ALPHA SUBUNIT)
  • PROTEIN (TELOMERE-BINDING PROTEIN BETA SUBUNIT)
KeywordsPROTEIN/DNA / SINGLE STRAND DNA BINDING PROTEIN / PROTEIN DNA INTERACTIONS / PROTEIN PROTEIN INTERACTIONS / OLIGONUCLEOTIDE AND OLIGOSACCHARIDE BINDING FOLD / OB FOLD / TELOMERES / PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


telomere cap complex / telomerase inhibitor activity / regulation of telomere maintenance via telomerase / nuclear telomere cap complex / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / telomere capping / protein-containing complex / nucleus
Similarity search - Function
Telomere-binding Protein Beta Subunit; Chain B / Telomere-binding Protein Beta Subunit; Chain / Telomere-binding protein subunit beta / Telomere-binding protein, beta subunit domain superfamily / Telomere-binding protein beta subunit (TEBP beta) / Telomere-binding protein, alpha subunit, Spirotrichea / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 ...Telomere-binding Protein Beta Subunit; Chain B / Telomere-binding Protein Beta Subunit; Chain / Telomere-binding protein subunit beta / Telomere-binding protein, beta subunit domain superfamily / Telomere-binding protein beta subunit (TEBP beta) / Telomere-binding protein, alpha subunit, Spirotrichea / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Telomere-binding protein subunit beta / Telomere-binding protein subunit alpha
Similarity search - Component
Biological speciesSterkiella nova (eukaryote)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.8 Å
AuthorsHorvath, M.P. / Schweiker, V.L. / Bevilacqua, J.M. / Ruggles, J.A. / Schultz, S.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand DNA.
Authors: Horvath, M.P. / Schweiker, V.L. / Bevilacqua, J.M. / Ruggles, J.A. / Schultz, S.C.
History
DepositionNov 25, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')
A: PROTEIN (TELOMERE-BINDING PROTEIN ALPHA SUBUNIT)
B: PROTEIN (TELOMERE-BINDING PROTEIN BETA SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)88,6903
Polymers88,6903
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.500, 94.500, 426.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Cell settinghexagonal
Space group name H-MP6122

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Components

#1: DNA chain DNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')


Mass: 3805.460 Da / Num. of mol.: 1 / Fragment: SINGLE STRAND DODECAMER DNA / Source method: obtained synthetically
#2: Protein PROTEIN (TELOMERE-BINDING PROTEIN ALPHA SUBUNIT) / ALPHA SUBUNIT


Mass: 56168.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ALANINE VERSION / Source: (gene. exp.) Sterkiella nova (eukaryote) / Gene: MAC-56A / Organelle: MACRONUCLEOUS / Plasmid: PKKT7-H / Gene (production host): MAC-56A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P29549
#3: Protein PROTEIN (TELOMERE-BINDING PROTEIN BETA SUBUNIT) / BETA SUBUNIT


Mass: 28716.672 Da / Num. of mol.: 1 / Fragment: N-TERMINAL 28 KDA CORE DOMAIN
Source method: isolated from a genetically manipulated source
Details: ALANINE VERSION / Source: (gene. exp.) Sterkiella nova (eukaryote) / Gene: MAC-41A / Organelle: MACRONUCLEOUS
Plasmid details: GENE WAS TRUNCTATED TO PRODUCE THE N-TERMINAL 28 KDA CORE DOMAIN ENDING WITH RESIDE LEU B 260
Plasmid: PKKT7-H / Gene (production host): MAC-41A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P16458
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1NACL11
2EDTA11
3NAN311
4DTT11
5ETHYLENE GLYCOL12
6PEG 400012
7MES12
Crystal grow
*PLUS
Details: drop contains the same amount of reservoir solution except 50mM NaCl
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.2 Malpha subunit1drop
450 mM1dropNaCl
55 mMTris-HCl1drop
60.1 mMEDTA1drop
70.02 %1dropNaN3
82 mMdithiothreitol1drop
930 %ethylene glycol1reservoir
2beta subunit1drop1.0-1.5 equivalents each of
3ssDNA1drop
103-8 %PEG40001reservoir
1140 mMMES1reservoir
120.02 %1reservoirNaN3
132 mMdithiothreitol1reservoir
1450 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 1, 1994 / Details: YALE MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 24061 / % possible obs: 82.5 % / Redundancy: 2.9 % / Biso Wilson estimate: 6.9 Å2 / Rsym value: 0.084 / Net I/σ(I): 10.3
Reflection shellResolution: 2.8→2.98 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.498 / % possible all: 57.1
Reflection
*PLUS
Num. measured all: 70514 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 57.1 % / Rmerge(I) obs: 0.498

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 328629.15 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.292 2376 9.9 %RANDOM
Rwork0.251 ---
obs0.251 23908 82.7 %-
all-23908 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.26 e/Å3
Displacement parametersBiso mean: 37.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5404 253 0 23 5680
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.031.5
X-RAY DIFFRACTIONc_mcangle_it3.542
X-RAY DIFFRACTIONc_scbond_it2.532
X-RAY DIFFRACTIONc_scangle_it4.052.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 273 10.1 %
Rwork0.361 2432 -
obs--57.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88
LS refinement shell
*PLUS
Rfactor obs: 0.361

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