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- PDB-6ros: REP related 18-mer DNA -

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Basic information

Entry
Database: PDB / ID: 6ros
TitleREP related 18-mer DNA
ComponentsREP related 18-mer DNA from C. hominis
KeywordsDNA / A-DNA / Duplex / non-canonical pairing / T-T mismatch / REP / Cardiobacterium hominis
Function / homologySTRONTIUM ION / DNA / DNA (> 10)
Function and homology information
Biological speciesCardiobacterium hominis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKolenko, P. / Svoboda, J. / Schneider, B.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Ministry of Education (Czech Republic)CZ.02.1.01/0.0/0.0/16_013/0001776) Czech Republic
Ministry of Education (Czech Republic)CZ.02.1.01/0.0/0.0/16_019/0000778 Czech Republic
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches.
Authors: Kolenko, P. / Svoboda, J. / Cerny, J. / Charnavets, T. / Schneider, B.
History
DepositionMay 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 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: REP related 18-mer DNA from C. hominis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7724
Polymers5,5101
Non-polymers2633
Water00
1
A: REP related 18-mer DNA from C. hominis
hetero molecules

A: REP related 18-mer DNA from C. hominis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5458
Polymers11,0192
Non-polymers5266
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area2700 Å2
ΔGint-130 kcal/mol
Surface area6230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.440, 38.440, 89.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-101-

SR

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Components

#1: DNA chain REP related 18-mer DNA from C. hominis


Mass: 5509.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Cardiobacterium hominis (bacteria)
#2: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Sr

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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: 59.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Natrix crystallization screen (Hampton Research) precipitant 22-26% (+/-)-2-Methyl-2,4-pentanediol buffer 0.04 M Sodium cacodylate trihydrate salt 0.04 M Magnezium chloride hexahydrate 0.08 ...Details: Natrix crystallization screen (Hampton Research) precipitant 22-26% (+/-)-2-Methyl-2,4-pentanediol buffer 0.04 M Sodium cacodylate trihydrate salt 0.04 M Magnezium chloride hexahydrate 0.08 M Strontium chloride hexahydrate additive 0.012 M spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.979491 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 8, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979491 Å / Relative weight: 1
ReflectionResolution: 2.7→44.8 Å / Num. obs: 2126 / % possible obs: 99.9 % / Redundancy: 22.5 % / Biso Wilson estimate: 88 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.062 / Χ2: 1.01 / Net I/σ(I): 24.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 23.9 % / Rmerge(I) obs: 1.811 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 290 / CC1/2: 0.869 / Rpim(I) all: 0.372 / Rrim(I) all: 1.85 / Χ2: 0.98 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14rc3_3199: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Deposition ID D_1200013700

Resolution: 2.7→35.325 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.75
Details: Refined against non-anomalous structure factors (F_XDSdataset,SIGF_XDSdataset)
RfactorNum. reflection% reflectionSelection details
Rfree0.2786 95 5 %RANDOM
Rwork0.2419 ---
obs0.2498 2089 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 108 Å2
Refinement stepCycle: LAST / Resolution: 2.7→35.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 365 3 0 368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011408
X-RAY DIFFRACTIONf_angle_d1.09628
X-RAY DIFFRACTIONf_dihedral_angle_d21.266176
X-RAY DIFFRACTIONf_chiral_restr0.05271
X-RAY DIFFRACTIONf_plane_restr0.00618
LS refinement shellHighest resolution: 2.7 Å

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