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- PDB-7z7m: REP-related Chom18 variant with double CC mismatch -

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Basic information

Entry
Database: PDB / ID: 7z7m
TitleREP-related Chom18 variant with double CC mismatch
ComponentsChom18-CC DNA
KeywordsDNA / Mismatch / Non-canonical / Base pair / Double helix
Function / homologySTRONTIUM ION / DNA / DNA (> 10)
Function and homology information
Biological speciesCardiobacterium hominis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSvoboda, J. / Schneider, B. / Berdar, D. / Kolenko, P.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLTAUSA18197 Czech Republic
Czech Academy of SciencesRVO 86652036 Czech Republic
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Conformation-based refinement of 18-mer DNA structures.
Authors: Svoboda, J. / Berdar, D. / Kolenko, P. / Cerny, J. / Novakova, Z. / Pavlicek, J. / Schneider, B.
History
DepositionMar 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chom18-CC DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5672
Polymers5,4801
Non-polymers881
Water00
1
A: Chom18-CC DNA
hetero molecules

A: Chom18-CC DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1344
Polymers10,9592
Non-polymers1752
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area2170 Å2
ΔGint-66 kcal/mol
Surface area6340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.090, 38.090, 87.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: DNA chain Chom18-CC DNA


Mass: 5479.518 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.: 1 / Source method: obtained synthetically / Formula: Sr
Has ligand of interestN

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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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Natrix crystallization screen (Hampton Research) precipitant 18-22% (+/-)-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 18-22% (+/-)-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: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.3418 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Apr 15, 2021
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 2.4→28.72 Å / Num. obs: 2658 / % possible obs: 94.4 % / Redundancy: 32.7 % / Biso Wilson estimate: 66.89 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.012 / Rrim(I) all: 0.064 / Χ2: 1.08 / Net I/σ(I): 35.7
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 33.2 % / Rmerge(I) obs: 1.314 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 301 / CC1/2: 0.9 / Rpim(I) all: 0.229 / Rrim(I) all: 1.334 / Χ2: 0.69 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ROS

6ros


Resolution: 2.6→28.72 Å / SU ML: 0.4592 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.5453
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2921 88 4.2 %Random
Rwork0.2326 0 --
obs0.2379 2092 92.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.98 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 363 1 0 364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0108406
X-RAY DIFFRACTIONf_angle_d1.2773624
X-RAY DIFFRACTIONf_chiral_restr0.072471
X-RAY DIFFRACTIONf_plane_restr0.005118
X-RAY DIFFRACTIONf_dihedral_angle_d17.6647176
LS refinement shellResolution: 2.6→2.69 Å
RfactorNum. reflection% reflection
Rfree0.6781 5 2.2 %
Rwork0.3798 220 -
obs--100 %

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