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

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Basic information

Entry
Database: PDB / ID: 6gdh
TitleHolliday Junctions formed from Telomeric DNA
Components
  • DNA (5'-D(*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')
  • DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
KeywordsRECOMBINATION / Holliday junction / Homologous recombination / Telomeres / ALT mechanism / ACC structural motif.
Function / homologyDNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 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 23, 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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')
B: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
C: DNA (5'-D(*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')
D: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
E: DNA (5'-D(*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')
F: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
G: DNA (5'-D(*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')
H: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)24,3528
Polymers24,3528
Non-polymers00
Water00
1
A: DNA (5'-D(*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')
B: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
C: DNA (5'-D(*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')
D: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)12,1764
Polymers12,1764
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')
F: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
G: DNA (5'-D(*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')
H: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)12,1764
Polymers12,1764
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.733, 33.161, 83.467
Angle α, β, γ (deg.)99.870, 90.070, 110.940
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain
DNA (5'-D(*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')


Mass: 2972.982 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain
DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')


Mass: 3115.050 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: 2.48 Å3/Da / Density % sol: 50.33 % / Description: Flat plate, hexagonal
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25 mM potassium chloride, 10 mM potassium cacodylate 50mM for magnesium chloride, 20mM for calcium chloride, MPD 32% to 38%
Temp details: fixed

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.5418 Å
DetectorType: AGILENT TITAN CCD / Detector: CCD / Date: Nov 12, 2014 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→22.51 Å / Num. obs: 5625 / % possible obs: 97.8 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.037 / Rrim(I) all: 0.07 / Net I/σ(I): 11.4 / Num. measured all: 19984 / Scaling rejects: 76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.8-2.952.60.4478130.9150.3240.55593.6
8.86-22.513.90.0261690.9990.0160.03188.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefmac_5.8.0222refinement
Aimless0.6.3data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
CrysalisPro1.171.36.32data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HS1

3hs1


Resolution: 2.85→22.51 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.93 / Matrix type: sparse / SU B: 21.339 / SU ML: 0.392 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0 / ESU R Free: 0.444
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2729 223 4.1 %RANDOM
Rwork0.228 ---
obs0.2298 5155 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 88.14 Å2 / Biso mean: 42.612 Å2 / Biso min: 10.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-4.46 Å20.83 Å2
2---8.25 Å23.21 Å2
3---11.52 Å2
Refinement stepCycle: final / Resolution: 2.85→22.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1616 0 0 1616
Num. residues----80
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0111808
X-RAY DIFFRACTIONr_bond_other_d0.0050.02912
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.1712776
X-RAY DIFFRACTIONr_angle_other_deg1.83532160
X-RAY DIFFRACTIONr_chiral_restr0.1170.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02952
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02384
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
2.85-2.9240.507180.45338241895.6940.44
2.924-3.0040.351120.43239141497.3430.415
3.004-3.0910.609170.34732934999.140.339
3.091-3.1860.542110.27934736797.5480.298
3.186-3.290.193140.16836738499.2190.21
3.29-3.4060.318110.21433034399.4170.25
3.406-3.5340.403120.29331032798.4710.283
3.534-3.6780.397180.27832434499.4190.278
3.678-3.8410.324160.26227229298.630.266
3.841-4.0280.1450.241292300990.254
4.028-4.2450.212160.21426027799.6390.22
4.245-4.5020.23750.19324825798.4440.189
4.502-4.8120.154130.21726728199.6440.207
4.812-5.1960.34170.20919621599.070.204
5.196-5.690.229130.220521999.5430.2
5.69-6.3570.19480.16117718798.930.168
6.357-7.3340.17140.16316416999.4080.187
7.334-8.9640.20840.1314214898.6490.178
8.964-12.6020.11380.13710411795.7260.192
12.602-82.0410.43910.173476376.190.247

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