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- PDB-1k8g: Crystal Structure of the N-terminal domain of Oxytricha nova telo... -

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Basic information

Entry
Database: PDB / ID: 1k8g
TitleCrystal Structure of the N-terminal domain of Oxytricha nova telomere end binding protein alpha subunit both uncomplexed and complexed with telomeric ssDNA
Components
  • 5'-D(TP*TP*GP*GP*GP*G)-3'
  • Telomere-Binding Protein alpha Subunit
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA Complex / telomeres / sequence specific ssDNA binding protein / OB folds / protein single strand DNA interactions / 3'-DNA end binding protein / telomere end binding protein / DNA BINDING 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
Similarity search - Function
Telomere-binding protein, alpha subunit, Spirotrichea / : / Telomere end-binding protein alpha subunit OB2 domain / 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 ...Telomere-binding protein, alpha subunit, Spirotrichea / : / Telomere end-binding protein alpha subunit OB2 domain / 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 / Telomere-binding protein subunit alpha
Similarity search - Component
Biological speciesSterkiella nova (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsClassen, S. / Ruggles, J.A. / Schultz, S.C.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of the N-terminal domain of Oxytricha nova telomere end-binding protein alpha subunit both uncomplexed and complexed with telomeric ssDNA.
Authors: Classen, S. / Ruggles, J.A. / Schultz, S.C.
History
DepositionOct 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
D: 5'-D(TP*TP*GP*GP*GP*G)-3'
E: 5'-D(TP*TP*GP*GP*GP*G)-3'
A: Telomere-Binding Protein alpha Subunit
B: Telomere-Binding Protein alpha Subunit
C: Telomere-Binding Protein alpha Subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,41711
Polymers112,8415
Non-polymers5766
Water3,297183
1
D: 5'-D(TP*TP*GP*GP*GP*G)-3'
A: Telomere-Binding Protein alpha Subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4324
Polymers38,2402
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(TP*TP*GP*GP*GP*G)-3'
B: Telomere-Binding Protein alpha Subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4324
Polymers38,2402
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Telomere-Binding Protein alpha Subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5523
Polymers36,3601
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.182, 121.182, 137.169
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 1880.251 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Telomere-Binding Protein alpha Subunit / alpha / macronuclear alpha protein (alanine version) / MAC-56A


Mass: 36360.074 Da / Num. of mol.: 3 / Fragment: N-terminal 35kDa ssDNA binding domain
Source method: isolated from a genetically manipulated source
Details: alanine version / Source: (gene. exp.) Sterkiella nova (eukaryote) / Plasmid: pKKT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P29549
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.5 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, MES, Ammonium sulfate, DTT, Sodium Azide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG400011
2MES11
3NH4SO411
4DTT11
5Sodium Azide11
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mMTris1droppH7.5
250 mM1dropNaCl
32 mMdithiothreitol1drop
40.1 mMEDTA1drop
50.02 %1dropNaN3
622 %(w/v)PEG40001reservoir
750 mMMES1reservoirpH6.6
8150 mMammonium sulfate1reservoir
92 mMdithiothreitol1reservoir
100.02 %1reservoirNaN3
1150 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 1999
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 35994 / Num. obs: 35994 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 38.8 Å2 / Rsym value: 0.103 / Net I/σ(I): 20.3
Reflection shellResolution: 2.6→30 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.71 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 574134 / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.71

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: residues 37-320 of Oxytricha nova telomere end binding protein alpha subunit PDB accession 1OTC

1otc


Resolution: 2.6→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 213150.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS automatically determined
RfactorNum. reflection% reflectionSelection details
Rfree0.285 3583 10 %RANDOM
Rwork0.246 ---
all0.246 35994 --
obs0.246 35994 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.7033 Å2 / ksol: 0.336706 e/Å3
Displacement parametersBiso mean: 46.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.75 Å28.23 Å20 Å2
2--5.75 Å20 Å2
3----11.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6657 170 30 183 7040
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it1.621.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 574 10 %
Rwork0.328 5143 -
obs--95.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / Num. reflection obs: 35965 / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 46.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.557
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
X-RAY DIFFRACTIONc_mcbond_it1.621.5
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Rfactor Rfree: 0.393 / % reflection Rfree: 10 % / Rfactor Rwork: 0.328 / Rfactor obs: 0.339

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