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- PDB-1jb7: DNA G-Quartets in a 1.86 A Resolution Structure of an Oxytricha n... -

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Basic information

Entry
Database: PDB / ID: 1jb7
TitleDNA G-Quartets in a 1.86 A Resolution Structure of an Oxytricha nova Telomeric Protein-DNA Complex
Components
  • (telomere-binding protein ...) x 2
  • 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
KeywordsDNA-BINDING PROTEIN/DNA / telomere-binding protein / DNA-protein interactions / DNA hydration / sodium ion / quadruplex 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: 1.86 Å
AuthorsHorvath, M.P. / Schultz, S.C.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: DNA G-quartets in a 1.86 A resolution structure of an Oxytricha nova telomeric protein-DNA complex.
Authors: Horvath, M.P. / 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: Structure / Year: 1994
Title: Refined Solution Structure of the Dimeric Quadruplex Formed from the Oxytricha Telomeric Oligonucleotide d(GGGGTTTTGGGG)
Authors: Schultze, P. / Smith, F.W. / Feigon, J.
History
DepositionJun 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 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 / 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*GP*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)96,42910
Polymers96,3015
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)93.100, 93.100, 421.800
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-753-

HOH

21A-755-

HOH

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Components

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DNA chain , 1 types, 3 molecules DGH

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


Mass: 3805.460 Da / Num. of mol.: 3 / 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

#2: Protein telomere-binding protein 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 / Plasmid: pKKT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P29549
#3: Protein telomere-binding protein beta subunit


Mass: 28716.672 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 / 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

#4: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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: 3

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, ethylene glycol, sodium chloride, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 282K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2ethylene glycol11
3NaCl11
4MES11
Crystal grow
*PLUS
pH: 6
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 1999 / Details: Bent 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: 1.86→20 Å / Num. all: 92896 / Num. obs: 92060 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.9
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.2 / Num. unique all: 8678 / % possible all: 95.6
Reflection
*PLUS
Num. measured all: 903239

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OTC

1otc


Resolution: 1.86→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 418030.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
Details: 'Molecular replacement' consisted of rigid-body refinement of the 2.8 A room-temperature structure. G-quartet linked DNA dimer was built into 2Fo-Fc and Fo-Fc electron density maps one ...Details: 'Molecular replacement' consisted of rigid-body refinement of the 2.8 A room-temperature structure. G-quartet linked DNA dimer was built into 2Fo-Fc and Fo-Fc electron density maps one nucleotide at a time so as to avoid preconceived notions of strand topology. Used maximum likelihood intensities target for refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.246 9022 9.9 %RANDOM
Rwork0.23 ---
all0.232 92052 --
obs0.232 91188 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.61 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso mean: 36.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.86→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5438 759 5 503 6705
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it1.672
X-RAY DIFFRACTIONc_scangle_it2.462.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree error% reflection obs (%)
1.86-1.980.33314199.80.3212130090.008896.05
1.98-2.130.29414550.27750.007798.46
2.13-2.340.287114850.26630.007599.89
2.34-2.680.276815010.2480.007199.98
2.68-3.380.243315750.22540.006199.98
3.38-200.214315870.20250.005499.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.23 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.25
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.333 / % reflection Rfree: 9.8 %

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