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- PDB-5mvp: Crystal structure of an A-DNA dodecamer containing the GGGCCC motif -

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Basic information

Entry
Database: PDB / ID: 5mvp
TitleCrystal structure of an A-DNA dodecamer containing the GGGCCC motif
ComponentsDNA
KeywordsDNA / A-DNA / Unmodified / Self-complementary
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.606 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 17, 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 1.6Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: DNA
B: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3663
Polymers7,3272
Non-polymers391
Water1,35175
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-4 kcal/mol
Surface area4350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.256, 43.256, 61.552
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: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Sodium chloride (80 mM) Potassium chloride (12 mM) Magnesium chloride (20 mM) Spermine tetrahydrochloride (12 mM) Sodium cacodylate (40 mM, pH 7.0) MPD (45% v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.606→37.461 Å / Num. obs: 9111 / % possible obs: 99.7 % / Redundancy: 6.3 % / Net I/σ(I): 23

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MVL

5mvl


Resolution: 1.606→37.461 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.97
RfactorNum. reflection% reflection
Rfree0.2089 456 5.02 %
Rwork0.153 --
obs0.1557 9075 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.606→37.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 1 75 562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014544
X-RAY DIFFRACTIONf_angle_d1.19836
X-RAY DIFFRACTIONf_dihedral_angle_d12.909232
X-RAY DIFFRACTIONf_chiral_restr0.08194
X-RAY DIFFRACTIONf_plane_restr0.01124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6056-1.8380.23851670.20092776X-RAY DIFFRACTION99
1.838-2.31560.26231510.19472848X-RAY DIFFRACTION100
2.3156-37.4710.19291380.14012995X-RAY DIFFRACTION100

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