[English] 日本語
Yorodumi
- PDB-1mic: GRAMICIDIN A: LEFT-HANDED PARALLEL DOUBLE HELICAL FORM IN METHANO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mic
TitleGRAMICIDIN A: LEFT-HANDED PARALLEL DOUBLE HELICAL FORM IN METHANOL IN THE PRESENCE OF CACL2, NMR, 20 STRUCTURES
ComponentsGRAMICIDIN A
KeywordsANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / DOUBLE HELIX / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN
Function / homologyGRAMICIDIN A / :
Function and homology information
Biological speciesBREVIBACILLUS BREVIS (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsChen, Y. / Tucker, A. / Wallace, B.A.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: Solution Structure of a Parallel Left-Handed Double-Helical Gramicidin-A Determined by 2D 1H NMR.
Authors: Chen, Y. / Tucker, A. / Wallace, B.A.
History
DepositionMay 22, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Nov 1, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.process_site / _pdbx_struct_assembly.details ..._pdbx_database_status.process_site / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.6Aug 8, 2018Group: Data collection / Experimental preparation / Refinement description
Category: pdbx_nmr_details / pdbx_nmr_ensemble ...pdbx_nmr_details / pdbx_nmr_ensemble / pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_exptl_sample_conditions.label ..._pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pressure / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _pdbx_nmr_software.version
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GRAMICIDIN A
B: GRAMICIDIN A


Theoretical massNumber of molelcules
Total (without water)3,7652
Polymers3,7652
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 187structures with the lowest energy
RepresentativeModel #1

-
Components

#1: Protein/peptide GRAMICIDIN A / VALYL GRAMICIDIN


Type: Polypeptide / Class: Antibiotic / Mass: 1882.294 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: GRAMICIDIN A IS A HEXADECAMERIC HELICAL PEPTIDE WITH ALTERNATING D,L CHARACTERISTICS. THE N-TERM IS FORMYLATED (RESIDUE 0). THE C-TERM IS CAPPED WITH ETHANOLAMINE (RESIDUE 16).
Source: (natural) BREVIBACILLUS BREVIS (bacteria) / References: NOR: NOR00243, GRAMICIDIN A
Compound detailsGRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ...GRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ARE OBTAINED FROM BACILLUS BREVIS AND CALLED COLLECTIVELY GRAMICIDIN D HERE, GRAMICIDIN A IS REPRESENTED BY THE SEQUENCE (SEQRES)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TOCSY
121NOESY
131DQF-COSY

-
Sample preparation

DetailsType: solution / Contents: 20 mM Gramicidin D, 1 mM CaCl2, methanol / Label: sample_1 / Solvent system: methanol
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMGramicidin Dnatural abundance1
1 mMCaCl2natural abundance1
Sample conditionsLabel: sample_conditions / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
JEOL GXJEOLGX5002

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1BRUNGERstructure calculation
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 187 / Conformers submitted total number: 20

+
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