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- PDB-1kix: Dimeric Structure of the O. nova Telomere End Binding Protein Alp... -

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Basic information

Entry
Database: PDB / ID: 1kix
TitleDimeric Structure of the O. nova Telomere End Binding Protein Alpha Subunit with Bound ssDNA
Components
  • 5'-D(*T*TP*TP*TP*GP*GP*GP*G)-3'
  • Telomere-Binding Protein alpha Subunit
KeywordsDNA BINDING PROTEIN/DNA / TELOMERE BINDING PROTEIN / DNA-PROTEIN INTERACTIONS / SINGLE STRANDED DNA / ssDNA / 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 / 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: 2.7 Å
AuthorsPeersen, O.B. / Ruggles, J.A. / Schultz, S.C.
Citation
Journal: Nat.Struct.Biol. / Year: 2002
Title: Dimeric structure of the Oxytricha nova telomere end-binding protein alpha-subunit bound to ssDNA.
Authors: Peersen, O.B. / Ruggles, J.A. / Schultz, S.C.
#1: Journal: 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.
#2: Journal: 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
DepositionDec 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2002Provider: 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

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Assembly

Deposited unit
D: 5'-D(*T*TP*TP*TP*GP*GP*GP*G)-3'
A: Telomere-Binding Protein alpha Subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8494
Polymers58,6572
Non-polymers1922
Water1,54986
1
D: 5'-D(*T*TP*TP*TP*GP*GP*GP*G)-3'
A: Telomere-Binding Protein alpha Subunit
hetero molecules

D: 5'-D(*T*TP*TP*TP*GP*GP*GP*G)-3'
A: Telomere-Binding Protein alpha Subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,6988
Polymers117,3144
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_565z,-y+1,x1
Unit cell
Length a, b, c (Å)284.000, 284.000, 284.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432

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Components

#1: DNA chain 5'-D(*T*TP*TP*TP*GP*GP*GP*G)-3'


Mass: 2488.637 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 3' Terminal Single Strand DNA Sequence of Macronuclear Telomeres
#2: Protein Telomere-Binding Protein alpha Subunit / alpha / macronuclear alpha protein (alanine version) / MAC-56A


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 / 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.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 4.08 Å3/Da / Density % sol: 82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium Sulfate, Xylitol, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium Sulfate11
2Xylitol11
3HEPES11
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 mg/mlprotein1drop
220-50 %oligonucleotide1dropmolar excess
32.0-2.1 Mammonium sulfate1reservoir
45 %(w/v)xylitol1reservoir
550 mMHEPES1reservoirpH7.5
62 mMdithiothreitol1reservoir
70.02 %(w/v)sodium azide1reservoir

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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 2, 1999 / Details: BENY CONICAL SI MIRROR (RH COATING)
RadiationMonochromator: BENT CYLINDRICAL GE (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→35 Å / Num. obs: 27195 / % possible obs: 98.3 % / Redundancy: 5 % / Biso Wilson estimate: 51.5 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 16.1
Reflection shellResolution: 2.7→2.76 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2 / % possible all: 94.5
Reflection
*PLUS
Lowest resolution: 35 Å / Num. measured all: 135022
Reflection shell
*PLUS
Highest resolution: 2.7 Å / % possible obs: 94.5 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alpha N-terminal domains from alpha-beta-ssDNA complex (1OTC)

1otc


Resolution: 2.7→29.77 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 253035.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD BASED ON REFLECTION INTENSITIES
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2687 9.9 %RANDOM
Rwork0.208 ---
obs0.208 27046 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.5108 Å2 / ksol: 0.367888 e/Å3
Displacement parametersBiso mean: 43.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3605 136 10 86 3837
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.191.5
X-RAY DIFFRACTIONc_mcangle_it3.882
X-RAY DIFFRACTIONc_scbond_it2.862
X-RAY DIFFRACTIONc_scangle_it4.452.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 421 9.8 %
Rwork0.313 3885 -
obs--95.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 43.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
X-RAY DIFFRACTIONc_mcbond_it2.191.5
X-RAY DIFFRACTIONc_scbond_it2.862
X-RAY DIFFRACTIONc_mcangle_it3.882
X-RAY DIFFRACTIONc_scangle_it4.452.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.327 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.313

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