[English] 日本語
Yorodumi
- PDB-1mkl: NMR REFINED STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mkl
TitleNMR REFINED STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT IN A 5'-CPAFBG-3' SEQUENCE
Components
  • 5'-D(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3'
  • 5'-D(*AP*GP*AP*TP*CP*GP*AP*TP*GP*T)-3'
KeywordsDNA / Structure of the 8 / 9-Dihydro-8-(N7-guanyl)-9-hydroxy-aflatoxin B1 Adduct in a 5'-CpAFBG-3' Sequence context
Function / homology8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1 / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / Data was processed using felix 97. The NOE intensities were converted to distance using RANMARDI module of MARDIGRAS. Starting structures were built using InsightII. XPLOR was used for structural refinement. Final averaged structure was solvated using AMBER., MD simulated annealing was performed in presence of counter ions using SANDER protocol. The back calculations were performed using CORMA.
AuthorsGiri, I. / Jenkins, M.D. / Schnetz-Boutaud, N.C. / Stone, M.P.
CitationJournal: Chem.Res.Toxicol. / Year: 2002
Title: Structural refinement of the 8,9-dihydro-8-(N7-guanyl)-9-hydroxy-aflatoxin B(1) adduct in a 5'-Cp(AFB)G-3' sequence.
Authors: Giri, I. / Jenkins, M.D. / Schnetz-Boutaud, N.C. / Stone, M.P.
History
DepositionAug 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_mod_residue / pdbx_struct_oper_list / pdbx_validate_planes / struct_asym / struct_conn / struct_ref
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _ndb_struct_na_base_pair.i_label_comp_id / _ndb_struct_na_base_pair.pair_name / _ndb_struct_na_base_pair_step.i_label_comp_id_1 / _ndb_struct_na_base_pair_step.i_label_comp_id_2 / _ndb_struct_na_base_pair_step.step_name / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _struct_ref.pdbx_align_begin
Revision 2.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3'
B: 5'-D(*AP*GP*AP*TP*CP*GP*AP*TP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4183
Polymers6,0882
Non-polymers3301
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1simulated annealing structure, calculaed starting from energy minmized averaged structure from 20 final structures. the enrgy minimized structure was solvated, and md simulation annealing was performed in presence of counter ions

-
Components

#1: DNA chain 5'-D(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3'


Mass: 3003.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain 5'-D(*AP*GP*AP*TP*CP*GP*AP*TP*GP*T)-3'


Mass: 3084.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-AFN / 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1


Mass: 330.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14O7

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY

-
Sample preparation

Details
Solution-IDSolvent system
199.999% D2O
290% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.5 mL of 0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA at pD 7.2, in 99.999% D2O 7.2 1 atm283 K
20.5 mL of 0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 7.2, in 9:1 H2O:D2O 7.2 1 atm283 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Brukercollection
Felix97Accelrys Inc.processing
MARDIGRAS5.2Borgias, B. A., and James, T. L. (1990) MARDIGRAS- -a procedure for matrix analysis of relaxation for discerning geometry of an aqueous structure. J. Magn. Reson. 87, 475-487data analysis
X-PLOR3.851A.T.Brungerrefinement
CORMA5.2Keepers, J. W., and James, T. L. (1984)J. Magn. Reson. 87, 475-487.iterative matrix relaxation
Amber6Case, D. A., and Pearlman C. A., et al. (1999) Amber 6.0, University of California, San Francisco, CA.structure solution
RefinementMethod: Data was processed using felix 97. The NOE intensities were converted to distance using RANMARDI module of MARDIGRAS. Starting structures were built using InsightII. XPLOR was used for ...Method: Data was processed using felix 97. The NOE intensities were converted to distance using RANMARDI module of MARDIGRAS. Starting structures were built using InsightII. XPLOR was used for structural refinement. Final averaged structure was solvated using AMBER., MD simulated annealing was performed in presence of counter ions using SANDER protocol. The back calculations were performed using CORMA.
Software ordinal: 1
Details: The structures are based on 341 distance retraints, 38 empirical H-bond restraints, 17 sugar pucker restraints, and 89 empirical torsion angle restraints
NMR representativeSelection criteria: simulated annealing structure, calculaed starting from energy minmized averaged structure from 20 final structures. the enrgy minimized structure was solvated, and md simulation ...Selection criteria: simulated annealing structure, calculaed starting from energy minmized averaged structure from 20 final structures. the enrgy minimized structure was solvated, and md simulation annealing was performed in presence of counter ions
NMR ensembleConformers submitted total number: 1

+
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://pdbjlvh1.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