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- PDB-6cq3: Crystal structure of DNA dodecamer D(CGCGAATTCGCG) -

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Basic information

Entry
Database: PDB / ID: 6cq3
TitleCrystal structure of DNA dodecamer D(CGCGAATTCGCG)
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / dodecamer
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsDelgado, J.L. / Vance, N.R. / Kerns, R.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI08761 United States
CitationJournal: To Be Published
Title: Crystal structure of DNA dodecamer D(CGCGAATTCGCG)
Authors: Delgado, J.L. / Vance, N.R. / Kerns, R.J.
History
DepositionMar 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4596
Polymers7,3272
Non-polymers1324
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-17 kcal/mol
Surface area4770 Å2
Unit cell
Length a, b, c (Å)24.330, 40.510, 65.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10% (v/v) 2-Methyl-2,4-pentanediol, 40mM Sodium cacodylate trihydrate, 20mM Hexammine cobalt(III) chloride, 40mM Lithium chloride, 20mM Magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0008 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jan 25, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0008 Å / Relative weight: 1
ReflectionResolution: 1.3→34.384 Å / Num. obs: 16300 / % possible obs: 99.04 % / Redundancy: 9.6 % / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.021 / Rrim(I) all: 0.054 / Rsym value: 0.052 / Net I/σ(I): 25.8
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 47 / CC1/2: 0.779 / Rpim(I) all: 0.446 / Rrim(I) all: 0.887 / Rsym value: 0.815 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDS2018/01/26data reduction
SCALA3.3.22data scaling
PHASER2.5.7phasing
Coot0.8.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BNA

8bna


Resolution: 1.3→34.384 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1886 811 4.98 %
Rwork0.1488 --
obs0.1506 16300 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→34.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 4 173 663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011544
X-RAY DIFFRACTIONf_angle_d1.298836
X-RAY DIFFRACTIONf_dihedral_angle_d30.735232
X-RAY DIFFRACTIONf_chiral_restr0.06494
X-RAY DIFFRACTIONf_plane_restr0.02224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3001-1.38160.27081390.19622482X-RAY DIFFRACTION98
1.3816-1.48820.23251440.16292521X-RAY DIFFRACTION99
1.4882-1.6380.19821300.13342542X-RAY DIFFRACTION99
1.638-1.8750.17031310.11612591X-RAY DIFFRACTION99
1.875-2.36220.15991360.14752607X-RAY DIFFRACTION100
2.3622-34.39620.18991310.15582746X-RAY DIFFRACTION99

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