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- PDB-5mvk: Crystal structure of an unmodified A-DNA dodecamer containing 3 c... -

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Basic information

Entry
Database: PDB / ID: 5mvk
TitleCrystal structure of an unmodified A-DNA dodecamer containing 3 consecutive CpG steps
ComponentsDNA
KeywordsDNA / A-DNA / Unmodified / CpG
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.531 Å
AuthorsHardwick, J.S. / Ptchelkine, D. / Phillips, S.E.V. / Brown, T.
Funding support1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J001694/2
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: 5-Formylcytosine does not change the global structure of DNA.
Authors: Hardwick, J.S. / Ptchelkine, D. / El-Sagheer, A.H. / Tear, I. / Singleton, D. / Phillips, S.E.V. / Lane, A.N. / Brown, T.
History
DepositionJan 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
Revision 1.3Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.6May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA
B: DNA


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-2 kcal/mol
Surface area4460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.678, 43.678, 58.887
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: DNA chain DNA


Mass: 3663.392 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Sodium chloride (12 mM) Potassium chloride (80 mM) Sodium cacodylate (40 mM, pH 7.0) Spermine tetrahydrochloride (12 mM) MPD (40% v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.53→37.83 Å / Num. obs: 10206 / % possible obs: 99.87 % / Redundancy: 9.2 % / Net I/σ(I): 19.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.531→37.826 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.75
RfactorNum. reflection% reflectionSelection details
Rfree0.1877 491 4.81 %Random selection
Rwork0.1805 ---
obs0.1809 10206 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.531→37.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 67 553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014544
X-RAY DIFFRACTIONf_angle_d1.379836
X-RAY DIFFRACTIONf_dihedral_angle_d16.068232
X-RAY DIFFRACTIONf_chiral_restr0.07394
X-RAY DIFFRACTIONf_plane_restr0.01324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5306-1.68470.27111320.23792378X-RAY DIFFRACTION100
1.6847-1.92840.3021960.20342395X-RAY DIFFRACTION100
1.9284-2.42950.27081300.23572424X-RAY DIFFRACTION100
2.4295-37.83780.15271330.15892518X-RAY DIFFRACTION100
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)
12.9483-2.6052-0.60943.6329-0.11490.4199-0.15460.10140.05730.0340.1153-0.1101-0.09750.01070.03780.2674-0.0347-0.03240.21640.0060.2652-10.470720.21852.5065
22.6914-1.3139-0.52927.6520.17630.25760.0145-0.11890.15620.44860.0828-0.21780.06930.0005-0.07050.242-0.0373-0.01810.2053-0.00790.1689-8.434316.43086.6048
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 12 )

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