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- PDB-1ph3: CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROT... -

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Basic information

Entry
Database: PDB / ID: 1ph3
TitleCRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGTG
Components
  • (Telomere-binding protein ...) x 2
  • 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*T)-3'
  • 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*TP*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: 2.3 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 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 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
G: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*T)-3'
D: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*TP*G)-3'
H: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*T)-3'
A: Telomere-binding protein alpha subunit
B: Telomere-binding protein beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0399
Polymers88,9475
Non-polymers924
Water9,062503
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.636, 93.636, 423.111
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-749-

HOH

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Components

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DNA chain , 2 types, 3 molecules GHD

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


Mass: 4109.652 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: CHAINS G AND H ARE A G-QUARTET LINKED DNA DIMER. 3' TERMINAL SINGLE STRAND DNA SEQUENCE OF MACRONUCLEAR TELOMERES.
#2: DNA chain 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*TP*G)-3'


Mass: 3780.447 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: CHAIN D IS SINGLE STRAND DNA. 3' TERMINAL SINGLE STRAND DNA SEQUENCE OF MACRONUCLEAR TELOMERES, G TO T SUBSTITUTION.

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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: residues 9-224
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 , 2 types, 507 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: 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: 3 Å3/Da / Density % sol: 58.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
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: 83 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→24.82 Å / Num. all: 54758 / Num. obs: 49804 / Biso Wilson estimate: 24.7 Å2
Reflection
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.056

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→24.82 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 298435.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.263 4954 9.9 %RANDOM
Rwork0.23 ---
all0.233 54758 --
obs0.23 49804 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.4121 Å2 / ksol: 0.314343 e/Å3
Displacement parametersBiso mean: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.14 Å21.33 Å20 Å2
2--4.14 Å20 Å2
3----8.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.3→24.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5439 757 4 503 6703
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.362
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.842.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 811 10.1 %
Rwork0.311 7186 -
obs--98.1 %
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
Refinement
*PLUS
Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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