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- PDB-6gn2: Racemic crystal structure of A-DNA duplex formed from d(CCCGGG) i... -

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Basic information

Entry
Database: PDB / ID: 6gn2
TitleRacemic crystal structure of A-DNA duplex formed from d(CCCGGG) in space group R3
ComponentsDNA (5'-D(*CP*CP*CP*GP*GP*G)-3')
KeywordsDNA / Racemate
Function / homologytrimethylamine oxide / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.48 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 1.1Jan 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 1.2Jun 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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3916
Polymers7,2414
Non-polymers1502
Water88349
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)3,7714
Polymers3,6202
Non-polymers1502
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')


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.413, 105.413, 56.131
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number148
Space group name H-MH-3

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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.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-TMO / trimethylamine oxide / Trimethylamine N-oxide


Mass: 75.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9NO
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 4.14 Å3/Da / Density % sol: 70.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Ammonium sulfate, Tris / PH range: 8.5

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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: Jul 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.48→23.91 Å / Num. obs: 8101 / % possible obs: 97 % / Redundancy: 1.9 % / Biso Wilson estimate: 49.67 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0574 / Rrim(I) all: 0.08117 / Net I/σ(I): 10.71
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.4249 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 729 / CC1/2: 0.926 / Rrim(I) all: 0.6009 / % possible all: 89

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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: 2.48→23.91 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.67
RfactorNum. reflection% reflection
Rfree0.2723 809 10.12 %
Rwork0.2586 --
obs0.2601 7997 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.27 Å2
Refinement stepCycle: LAST / Resolution: 2.48→23.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 480 10 49 539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003544
X-RAY DIFFRACTIONf_angle_d0.392832
X-RAY DIFFRACTIONf_dihedral_angle_d12.629224
X-RAY DIFFRACTIONf_chiral_restr0.01492
X-RAY DIFFRACTIONf_plane_restr0.00124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4801-2.63540.4341250.37321126X-RAY DIFFRACTION92
2.6354-2.83860.33841420.39641232X-RAY DIFFRACTION99
2.8386-3.12390.36381320.31391220X-RAY DIFFRACTION99
3.1239-3.5750.30561410.24071203X-RAY DIFFRACTION97
3.575-4.50040.21271360.21741204X-RAY DIFFRACTION98
4.5004-26.35470.20061330.21421203X-RAY DIFFRACTION97
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)
14.31313.2099-2.655.6023-6.90679.20470.0389-0.12940.27-0.25530.0124-0.0359-1.49080.1454-0.14680.4437-0.05070.04110.1925-0.08320.384274.517374.99248.2679
22.22080.02712.8030.06620.66669.2950.0770.0009-0.08880.18160.2219-0.3115-0.12530.3125-0.37380.3618-0.03990.02330.1782-0.03250.391477.191668.194910.3815
34.04683.2967-0.9177.1175-2.22192.96210.17690.2998-0.12240.1765-0.3185-0.557-0.0930.29510.1030.24970.08030.00370.28150.03160.343781.844866.5355-3.8721
43.2198-3.1265-2.69929.71797.27675.72150.30320.28260.2683-0.9078-0.19330.0704-0.804-0.1752-0.08340.32530.06430.01460.19780.05120.274175.914566.6237-7.8107
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 )

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