[English] 日本語
Yorodumi
- PDB-2m1p: [Aba5,14]BTD-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m1p
Title[Aba5,14]BTD-2
Components[Aba5,14]BTD-2
KeywordsANTIMICROBIAL PROTEIN / theta-defensin / cyclic peptides / cyclic cystine ladder / disulfide bond
Function / homology[Aba5,14]BTD-2
Function and homology information
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsConibear, A.C. / Rosengren, K. / Daly, N.L. / Troiera Henriques, S. / Craik, D.J.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The cyclic cystine ladder in theta-defensins is important for structure and stability, but not antibacterial activity.
Authors: Conibear, A.C. / Rosengren, K.J. / Daly, N.L. / Henriques, S.T. / Craik, D.J.
History
DepositionDec 4, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: [Aba5,14]BTD-2


Theoretical massNumber of molelcules
Total (without water)2,0551
Polymers2,0551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide [Aba5,14]BTD-2


Type: Cyclic peptide / Class: Antimicrobial / Mass: 2054.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid phase peptide synthesis / References: [Aba5,14]BTD-2

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: Head-to-tail (Arg-Gly) cyclic peptide. Residues 5 and 14 are replaced by alpha-aminobuytyric acid.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1322D 1H-13C HSQC
1412D DQF-COSY
1522D 1H-1H ECOSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [Aba5,14]BTD, 10 ug DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [Aba5,14]BTD, 10 ug DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.6 mM[Aba5,14]BTD-2-11
0.010 mg/mLDSS-21
0.6 mM[Aba5,14]BTD-2-32
0.010 mg/mLDSS-42
Sample conditionspH: 4 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002

-
Processing

NMR software
NameVersionDeveloperClassification
CcpNmr2.1CCPNdata analysis
CcpNmr2.1CCPNchemical shift assignment
CcpNmr2.1CCPNpeak picking
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNS2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: Structures were calculated using the scripts from the RECOORD database. Used to calculate preliminary structures
NMR constraintsNOE constraints total: 118 / NOE intraresidue total count: 62 / NOE long range total count: 12 / NOE medium range total count: 8 / NOE sequential total count: 36 / Hydrogen bond constraints total count: 16 / Protein chi angle constraints total count: 8 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 17 / Protein psi angle constraints total count: 16
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / 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://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