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- PDB-1vtf: STRUCTURE OF 5'-D(*(BRO)CP*GP*(BRO)CP*G)-3' IN COMPLEX WITH PROFLAVINE -

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Basic information

Entry
Database: PDB / ID: 1vtf
TitleSTRUCTURE OF 5'-D(*(BRO)CP*GP*(BRO)CP*G)-3' IN COMPLEX WITH PROFLAVINE
ComponentsDNA (5'-D(*(BRO)CP*GP*(BRO)CP*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED / DEOXYRIBONUCLEIC ACID
Function / homologyPROFLAVIN / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsWesthof, E. / Hosur, M.V. / Sundaralingam, M.
CitationJournal: Biochemistry / Year: 1988
Title: Nonintercalative binding of proflavin to Z-DNA: structure of a complex between d(5BrC-G-5BrC-G) and proflavin.
Authors: Westhof, E. / Hosur, M.V. / Sundaralingam, M.
History
DepositionDec 13, 1988Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / pdbx_entity_src_syn / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,9558
Polymers2,6992
Non-polymers1,2556
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.900, 17.900, 44.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 1349.610 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-PRL / PROFLAVIN


Mass: 209.247 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H11N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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

Crystal growMethod: liquid diffusion / pH: 7
Details: ACETONE, SODIUM CACODYLATE, pH 7.00, LIQUID DIFFUSION
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12WATER1311
25ACETONE1614
38SODIUM CACODYLATE1917

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Data collection

Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Observed criterion σ(I): 2

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2→4.5 Å / σ(F): 4 /
RfactorNum. reflection
obs0.269 474
Refinement stepCycle: LAST / Resolution: 2→4.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 162 96 1 259

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