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- PDB-6gn3: Racemic crystal structure of A-DNA duplex formed from d(CCCGGG) i... -

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Basic information

Entry
Database: PDB / ID: 6gn3
TitleRacemic crystal structure of A-DNA duplex formed from d(CCCGGG) in space group P21/n
ComponentsDNA (5'-D(*CP*CP*CP*GP*GP*G)-3')
KeywordsDNA / Racemate
Function / homology: / trimethylamine oxide / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMandal, P.K. / Collie, G.W. / Kauffmann, B. / Huc, I.
Funding support France, 1items
OrganizationGrant numberCountry
European Research CouncilERC-2012-AdG-320892 France
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Racemic crystal structures of A-DNA duplexes.
Authors: Mandal, P.K. / Collie, G.W. / Kauffmann, B. / Huc, I.
History
DepositionMay 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.details
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
Revision 1.3Jun 12, 2024Group: 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 / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,31513
Polymers10,8616
Non-polymers4547
Water1448
1
A: DNA (5'-D(*CP*CP*CP*GP*GP*G)-3')
B: DNA (5'-D(*CP*CP*CP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9056
Polymers3,6202
Non-polymers2844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*CP*CP*CP*GP*GP*G)-3')
D: DNA (5'-D(*CP*CP*CP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7154
Polymers3,6202
Non-polymers942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: DNA (5'-D(*CP*CP*CP*GP*GP*G)-3')
F: DNA (5'-D(*CP*CP*CP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6963
Polymers3,6202
Non-polymers751
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.883, 41.430, 71.958
Angle α, β, γ (deg.)90.00, 97.47, 90.00
Int Tables number14
Space group name H-MP121/n1

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Components

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


Mass: 1810.205 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Racemic DNA / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-TMO / trimethylamine oxide


Mass: 75.110 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H9NO
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.33 Å3/Da / Density % sol: 63.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Ammonium sulfate, MES buffer, cobalt chloride / PH range: 6.5

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5417 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.8→31.49 Å / Num. obs: 6839 / % possible obs: 99 % / Redundancy: 1.9 % / Biso Wilson estimate: 49.82 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.0729 / Rrim(I) all: 0.1032 / Net I/σ(I): 11.19
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3393 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 685 / CC1/2: 0.924 / Rrim(I) all: 0.4799 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VT5

1vt5


Resolution: 2.8→31.49 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.46
RfactorNum. reflection% reflectionSelection details
Rfree0.3182 683 10.04 %Random
Rwork0.2795 ---
obs0.2836 6804 98.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.17 Å2
Refinement stepCycle: LAST / Resolution: 2.8→31.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 720 23 8 751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007820
X-RAY DIFFRACTIONf_angle_d0.5611254
X-RAY DIFFRACTIONf_dihedral_angle_d14.448336
X-RAY DIFFRACTIONf_chiral_restr0.03138
X-RAY DIFFRACTIONf_plane_restr0.00336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-3.01610.52961360.41871215X-RAY DIFFRACTION99
3.0161-3.31940.35161380.31681238X-RAY DIFFRACTION99
3.3194-3.7990.37091380.28681242X-RAY DIFFRACTION100
3.799-4.78360.27941340.26081197X-RAY DIFFRACTION97
4.7836-31.49470.23491370.22761229X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.70380.4675-2.14351.3106-0.89392.782-0.3152-1.0104-0.36270.01250.07920.06870.1856-0.84990.22610.35310.0018-0.00670.592-0.02640.2583-75.7742-42.697910.9239
22.4552-1.9581-0.88852.4201-0.46932.4010.4423-0.29950.0514-0.32240.162-0.219-0.4071-0.2319-0.49640.2665-0.04880.04190.4473-0.06610.1929-76.2885-35.89287.6057
30.45470.20110.1167.5213.35771.4992-0.0306-0.48790.39251.19160.17620.30020.6101-0.036-0.19970.43860.04270.05910.5856-0.1190.354-83.5464-26.577621.4134
44.3861-2.4889-1.91366.22040.98690.8360.7586-0.25350.6116-0.6477-0.3827-0.6136-0.1652-0.8474-0.40170.4528-0.06680.11930.6519-0.13990.3052-81.1072-22.886415.4779
57.0431-0.37131.22212.6586-0.89234.0655-0.08350.2260.3844-0.2176-0.41430.8003-0.2828-0.65430.41920.55-0.01-0.11590.5569-0.13310.477-68.9895-23.097627.8493
62.50622.84280.94993.54071.17731.3635-0.18931.77790.0866-0.35380.1837-0.0983-0.10721.0060.41050.3322-0.0389-0.10251.2569-0.02090.4812-65.6542-25.117121.7371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 6 )
2X-RAY DIFFRACTION2chain 'B' and (resid 7 through 12 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 6 )
4X-RAY DIFFRACTION4chain 'D' and (resid 7 through 12 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 6 )
6X-RAY DIFFRACTION6chain 'F' and (resid 7 through 12 )

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