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- PDB-6gdn: Holliday Junctions formed from Telomeric DNA -

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Basic information

Entry
Database: PDB / ID: 6gdn
TitleHolliday Junctions formed from Telomeric DNA
ComponentsTelomere DNA (42-MER)
KeywordsRECOMBINATION / Holliday junction / Homologous recombination / Telomeres / ALT mechanism / ACC structural motif.
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsParkinson, G.N. / Haider, S. / Li, P. / Khiali, S. / Munnur, D. / Ramanathan, A.
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Holliday Junctions Formed from Human Telomeric DNA.
Authors: Haider, S. / Li, P. / Khiali, S. / Munnur, D. / Ramanathan, A. / Parkinson, G.N.
History
DepositionApr 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomere DNA (42-MER)
B: Telomere DNA (42-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8554
Polymers25,8072
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-4 kcal/mol
Surface area14590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.937, 45.374, 63.828
Angle α, β, γ (deg.)90.000, 101.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain Telomere DNA (42-MER)


Mass: 12903.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Human telomeric DNA sequence / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 2.75 Å3/Da / Density % sol: 55.28 % / Description: Large flat hexagonal plates
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.04 M Magnesium acetate tetrahydrate, 0.05 M Sodium cacodylate trihydrate, 30% v/v (+/-)-2-Methyl-2,4-pentanediol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 27, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.68→45.38 Å / Num. obs: 8053 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.033 / Rrim(I) all: 0.064 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.68-2.753.60.7515740.4590.4470.87799.8
11.99-45.383.50.01910610.0110.02298.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia20.5.474-gb1e580cd-dials-1.8data reduction
Aimless0.5.32data scaling
PHASERphasing
REFMACrefmac_5.8.0222refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DGH

6dgh
PDB Unreleased entry


Resolution: 3→45.38 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.903 / Matrix type: sparse / SU B: 22.957 / SU ML: 0.422 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0 / ESU R Free: 0.479
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.279 283 4.9 %RANDOM
Rwork0.2343 ---
obs0.2366 5446 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 120 Å2 / Biso mean: 68.308 Å2 / Biso min: 20.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å2-0 Å20.7 Å2
2---1.77 Å20 Å2
3---1.94 Å2
Refinement stepCycle: final / Resolution: 3→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1710 2 0 1712
Biso mean--54.69 --
Num. residues----84
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0111912
X-RAY DIFFRACTIONr_bond_other_d0.0090.02954
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.1822948
X-RAY DIFFRACTIONr_angle_other_deg2.37532270
X-RAY DIFFRACTIONr_chiral_restr0.1250.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02988
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02392
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
3-3.0780.428270.39238542297.630.363
3.078-3.1620.333120.33439441298.5440.303
3.162-3.2530.371190.21537440098.250.193
3.253-3.3530.207220.23735838498.9580.221
3.353-3.4620.258200.23435137499.1980.22
3.462-3.5830.393140.28235637598.6670.266
3.583-3.7170.412180.27731433698.810.263
3.717-3.8680.373140.26532534199.4130.248
3.868-4.0390.351160.25630532299.6890.242
4.039-4.2350.235180.2233023201000.213
4.235-4.4620.303130.21628029599.3220.209
4.462-4.730.347130.23826928499.2960.227
4.73-5.0530.231110.2226027399.2670.218
5.053-5.4530.19760.192352411000.188
5.453-5.9670.322150.1962092241000.199
5.967-6.6580.183120.2820421899.0830.287
6.658-7.6650.23780.22117918899.4680.224
7.665-9.3310.29130.211471601000.214
9.331-12.9630.2860.1712613399.2480.207
12.963-49.0170.09560.17971771000.203

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