[English] 日本語
Yorodumi
- PDB-1hvz: RTD-1, A CYCLIC ANTIMICROBIAL DEFENSIN FROM RHESUS MACAQUE LEUKOCYTES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hvz
TitleRTD-1, A CYCLIC ANTIMICROBIAL DEFENSIN FROM RHESUS MACAQUE LEUKOCYTES
ComponentsTHETA DEFENSIN 1
KeywordsANTIMICROBIAL PROTEIN / cyclic / beta-sheet / disulfide-rich
Function / homology:
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, explicit inclusion of water molecules
AuthorsCraik, D.J. / Trabi, M. / Schirra, H.J.
CitationJournal: Biochemistry / Year: 2001
Title: Three-dimensional structure of RTD-1, a cyclic antimicrobial defensin from Rhesus macaque leukocytes.
Authors: Trabi, M. / Schirra, H.J. / Craik, D.J.
History
DepositionJan 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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
Remark 999SEQUENCE RESIDUES NUMBERED ACCORDING TO TANG ET AL., SCIENCE 286 (1999), PP. 498-502

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THETA DEFENSIN 1


Theoretical massNumber of molelcules
Total (without water)2,1111
Polymers2,1111
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 / 100structures with the least restraint violations,structures with the lowest energy
Representative

-
Components

#1: Protein/peptide THETA DEFENSIN 1 / RTD-1


Mass: 2110.668 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. This sequence occurs naturally in rhesus macaques (mucaca mulatta)
References: GenBank: 7512249

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
133DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM RTD-1, 20mM sodium phosphate pH 4.5, 80% H2O, 10% D2O, 10% acetonitrile-d380% H2O, 10% D2O, 10% acetonitrile-d3
21mM RTD-1, 20mM sodium phosphate pH 4.5, 90% H2O, 10% D2O90% H2O/10% D2O
31mM RTD-1, 20mM sodium phosphate pH 4.5, 99% D2O99% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120mM sodium phosphate 4.5 ambient 310 K
220mM sodium phosphate 4.5 ambient 300 K
320mM sodium phosphate 4.5 ambient 280 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker ARXBrukerARX5002

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
CCNMRCieslar, Kalus & Holakdata analysis
X-PLOR3.851Brungerstructure solution
CNS1Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: torsion angle dynamics, simulated annealing, explicit inclusion of water molecules
Software ordinal: 1
Details: The structures are based on a total of 94 restraints, 87 are NOE-derived distance constraints, 7 dihedral angle restraints
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / 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