[English] 日本語
Yorodumi
- PDB-3ft6: Crystal Structure of Proflavine in Complex with a DNA hexamer duplex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ft6
TitleCrystal Structure of Proflavine in Complex with a DNA hexamer duplex
Components5'-D(*CP*GP*AP*TP*CP*G)-3'
KeywordsDNA / DNA Binding / Proflavine / Intercalator
Function / homologyCOBALT HEXAMMINE(III) / PROFLAVIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsMaehigashi, T. / Persil, O. / Hud, N.V. / Williams, L.D.
CitationJournal: To be Published
Title: Crystal Structure of Proflavine in Complex with a DNA hexamer duplex
Authors: Maehigashi, T. / Persil, O. / Hud, N.V. / Williams, L.D.
History
DepositionJan 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 6, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,5207
Polymers3,6182
Non-polymers9025
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-10 kcal/mol
Surface area3920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.563, 24.563, 78.276
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

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


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic Construct
#2: Chemical ChemComp-PRL / PROFLAVIN


Mass: 209.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11N3
#3: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: HEPES, Cobalt Hexamine, MPD, PEG1000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2MPD11
3PEG100011
4Cobalt Hexamine11
5HEPES12
6Cobalt Hexamine12
7MPD12
8PEG100012

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→21.27 Å / Num. all: 10189 / Num. obs: 10189 / % possible obs: 93.4 % / Redundancy: 9.1 % / Rsym value: 0.052 / Net I/σ(I): 44.8
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.75 / Num. unique all: 569 / Rsym value: 0.334 / % possible all: 52.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1Z3F (DNA only)

1z3f


Resolution: 1.12→20.53 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.652 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21929 1096 11.1 %RANDOM
Rwork0.18433 ---
obs0.18811 8808 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.446 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.12→20.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 53 37 330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021322
X-RAY DIFFRACTIONr_angle_refined_deg1.7323507
X-RAY DIFFRACTIONr_chiral_restr0.0910.246
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.02158
X-RAY DIFFRACTIONr_nbd_refined0.1320.2122
X-RAY DIFFRACTIONr_nbtor_refined0.3260.2158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.217
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.210
X-RAY DIFFRACTIONr_scbond_it2.3253559
X-RAY DIFFRACTIONr_scangle_it2.7824.5498
X-RAY DIFFRACTIONr_rigid_bond_restr1.9263559
X-RAY DIFFRACTIONr_sphericity_bonded5.273293
LS refinement shellResolution: 1.12→1.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 69 -
Rwork0.259 472 -
obs-472 73.41 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more