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- PDB-1pa6: Crystal structure of the OXYTRICHA nova telomere end-binding prot... -

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Basic information

Entry
Database: PDB / ID: 1pa6
TitleCrystal structure of the OXYTRICHA nova telomere end-binding protein complexed with noncognate ssDNA GGGGTTTTGAGG
Components
  • (Telomere-binding protein ...) x 2
  • 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*AP*GP*G)-3'
  • 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
KeywordsDNA BINDING PROTEIN/DNA / SINGLE STRAND DNA BINDING PROTEIN / PROTEIN DNA INTERACTIONS / SEQUENCE SPECIFICITY / NONCOGNATE / OLIGONUCLEOTIDE AND OLIGOSACCHARIDE BINDING FOLD / OB FOLD / TELOMERES / PROTEIN/DNA / 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 / 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 / : / Telomere end-binding protein alpha subunit OB2 domain / Protection of telomeres protein 1 / 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 / : / 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 / DNA (> 10) / Telomere-binding protein subunit beta / Telomere-binding protein subunit alpha
Similarity search - Component
Biological speciesSterkiella nova (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsTheobald, D.L. / Schultz, S.C.
CitationJournal: Embo J. / Year: 2003
Title: Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes
Authors: Theobald, D.L. / Schultz, S.C.
History
DepositionMay 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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

Downloads & links

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Assembly

Deposited unit
D: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*AP*GP*G)-3'
G: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
H: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
A: Telomere-binding protein alpha subunit
B: Telomere-binding protein beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,47610
Polymers88,3485
Non-polymers1275
Water9,062503
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.110, 93.110, 422.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-750-

HOH

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Components

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DNA chain , 2 types, 3 molecules DGH

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


Mass: 3789.461 Da / Num. of mol.: 1 / Mutation: G10A / Source method: obtained synthetically
Details: 3' TERMINAL SINGLE STRAND DNA SEQUENCE OF MACRONUCLEAR TELOMERES, G to A substitution
#2: DNA chain 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'


Mass: 3805.460 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: 3' TERMINAL SINGLE STRAND DNA SEQUENCE OF MACRONUCLEAR TELOMERES

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Telomere-binding protein ... , 2 types, 2 molecules AB

#3: Protein Telomere-binding protein alpha subunit / Telomere-binding protein 56 kDa subunit / TEBP alpha


Mass: 52460.027 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 AND MAC-56K AND MAC-56S / Plasmid: PKKT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P29549
#4: Protein Telomere-binding protein beta subunit / Telomere-binding protein 41 kDa subunit / TEBP beta


Mass: 24487.682 Da / Num. of mol.: 1 / Fragment: 28 KDA N-TERMINAL CORE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sterkiella nova (eukaryote) / Gene: MAC-41A AND MAC-41S / Plasmid: PKKT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P16458

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Non-polymers , 3 types, 508 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.98 Å3/Da / Density % sol: 58.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Horvath, M.P., (1998) Cell., 95, 963. / PH range low: 7 / PH range high: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 %ethylene glycol1drop
21-6 %PEG40001drop
340 mMMES1droppH5.5-7.0
40.02 %1dropNaN3
52 mMdithiothreitol1drop
650 mM1reservoirNaCl

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.45→29.79 Å / Num. obs: 31008 / Biso Wilson estimate: 35.4 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→29.79 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 95652.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 3083 9.9 %RANDOM
Rwork0.223 ---
all0.223 ---
obs0.264 31008 75.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.2595 Å2 / ksol: 0.291967 e/Å3
Displacement parametersBiso mean: 49.2 Å2
Baniso -1Baniso -2Baniso -3
1-10.09 Å2-1.24 Å20 Å2
2--10.09 Å20 Å2
3----20.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.45→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5439 758 5 503 6705
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.532
X-RAY DIFFRACTIONc_scbond_it1.742
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.394 416 9.5 %
Rwork0.336 3943 -
obs--65.2 %
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.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAMWATER.TOP
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93

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