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- PDB-5mvl: Crystal structure of an A-DNA dodecamer containing 5-bromouracil -

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Basic information

Entry
Database: PDB / ID: 5mvl
TitleCrystal structure of an A-DNA dodecamer containing 5-bromouracil
ComponentsBrominated DNA dodecamer
KeywordsDNA / A-DNA / 5-bromouracil / CpG
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.405 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Brominated DNA dodecamer
B: Brominated DNA dodecamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4813
Polymers7,4572
Non-polymers241
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint4 kcal/mol
Surface area4240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.517, 43.517, 60.850
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 Brominated DNA dodecamer


Mass: 3728.262 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.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Sodium chloride (80 mM) Potassium chloride (12 mM) Magnesium chloride (20 mM) Spermine tetrahydrochloride (12 mM) Sodium cacodylate (40 mM, pH 6.0) MPD (40 % v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.920, 1.240
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 10, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
21.241
ReflectionResolution: 1.405→23.673 Å / Num. obs: 13446 / % possible obs: 99.9 % / Redundancy: 9.3 % / Net I/σ(I): 23.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.405→23.673 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.17
RfactorNum. reflection% reflection
Rfree0.1823 771 5.73 %
Rwork0.1569 --
obs0.1584 13446 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.405→23.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 1 76 563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009544
X-RAY DIFFRACTIONf_angle_d1.067836
X-RAY DIFFRACTIONf_dihedral_angle_d15.645220
X-RAY DIFFRACTIONf_chiral_restr0.05592
X-RAY DIFFRACTIONf_plane_restr0.0124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4047-1.49270.26611190.19782065X-RAY DIFFRACTION99
1.4927-1.60790.15851490.14432061X-RAY DIFFRACTION100
1.6079-1.76970.15351240.11992081X-RAY DIFFRACTION100
1.7697-2.02570.20561290.1492106X-RAY DIFFRACTION100
2.0257-2.55160.20121250.19912132X-RAY DIFFRACTION100
2.5516-23.67660.17571250.14892230X-RAY DIFFRACTION100

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