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

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Basic information

Entry
Database: PDB / ID: 6rou
TitleREP related 18-mer DNA
ComponentsREP related 18-mer DNA from H. parasuis
KeywordsDNA / A-DNA / Duplex / non-canonical pairing / T-T mismatch / REP / Haemophilus parasuis
Function / homologySTRONTIUM ION / DNA / DNA (> 10)
Function and homology information
Biological speciesGlaesserella parasuis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.902 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:
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Assembly

Deposited unit
A: REP related 18-mer DNA from H. parasuis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6843
Polymers5,5091
Non-polymers1752
Water00
1
A: REP related 18-mer DNA from H. parasuis
hetero molecules

A: REP related 18-mer DNA from H. parasuis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3686
Polymers11,0172
Non-polymers3504
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area2160 Å2
ΔGint-73 kcal/mol
Surface area6290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.563, 38.563, 89.938
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 H. parasuis


Mass: 5508.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Glaesserella parasuis (bacteria)
#2: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 2 / 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: 58.96 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Natrix crystallization screen (Hampton Research) precipitant 30-32% (+/-)-2-Methyl-2,4-pentanediol buffer 0.04M Sodium cacodylate trihydrate salt 0.04 M Lithium chloride 0.08 M Strontium ...Details: Natrix crystallization screen (Hampton Research) precipitant 30-32% (+/-)-2-Methyl-2,4-pentanediol buffer 0.04M Sodium cacodylate trihydrate salt 0.04 M Lithium chloride 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: 2.9→44.97 Å / Num. obs: 1758 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 116 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.019 / Rrim(I) all: 0.064 / Χ2: 0.98 / Net I/σ(I): 20
Reflection shellResolution: 2.9→3.1 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 299 / CC1/2: 0.958 / Rpim(I) all: 0.188 / Rrim(I) all: 0.735 / Χ2: 0.88 / % 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: 2.902→35.442 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.46
RfactorNum. reflection% reflectionSelection details
Rfree0.3115 94 5.5 %RANDOM
Rwork0.264 ---
obs0.2721 1726 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 122 Å2
Refinement stepCycle: LAST / Resolution: 2.902→35.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 366 1 0 367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01408
X-RAY DIFFRACTIONf_angle_d1.015628
X-RAY DIFFRACTIONf_dihedral_angle_d22.366176
X-RAY DIFFRACTIONf_chiral_restr0.05271
X-RAY DIFFRACTIONf_plane_restr0.00518
LS refinement shellHighest resolution: 2.9 Å

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