[English] 日本語
Yorodumi
- PDB-3rdn: NMR STRUCTURE OF THE N-TERMINAL DOMAIN WITH A LINKER PORTION OF A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rdn
TitleNMR STRUCTURE OF THE N-TERMINAL DOMAIN WITH A LINKER PORTION OF ANTARCTIC EEL POUT ANTIFREEZE PROTEIN RD3, MINIMIZED AVERAGE STRUCTURE
ComponentsANTIFREEZE PROTEIN RD3 TYPE III
KeywordsANTIFREEZE / ANTIFREEZE PROTEIN / THERMAL HYSTERESIS PROTEIN / ICE BINDING PROTEIN
Function / homology
Function and homology information


extracellular region
Similarity search - Function
SAF domain / SAF / SAF domain / Antifreeze, type III / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ice-structuring protein RD3
Similarity search - Component
Biological speciesLycodichthys dearborni (Antarctic eel pout)
MethodSOLUTION NMR / SA
AuthorsMiura, K. / Ohgiya, S. / Hoshino, T. / Nemoto, N. / Hikichi, K. / Tsuda, S.
Citation
Journal: Nature / Year: 1996
Title: Structural basis for the binding of a globular antifreeze protein to ice.
Authors: Jia, Z. / DeLuca, C.I. / Chao, H. / Davies, P.L.
#1: Journal: Nature / Year: 1996
Title: Structural Basis for the Binding of a Globular Antifreeze Protein to Ice
Authors: Jia, Z. / Deluca, C.I. / Chao, H. / Davies, P.L.
#2: Journal: Structure / Year: 1996
Title: Refined Solution Structure of Type III Antifreeze Protein: Hydrophobic Groups May be Involved in the Energetics of the Protein-Ice Interaction
Authors: Sonnichsen, F.D. / Deluca, C.I. / Davies, P.L. / Sykes, B.D.
#3: Journal: Biochim.Biophys.Acta / Year: 1995
Title: Antifreeze Peptide Heterogeneity in an Antarctic Eel Pout Includes an Unusually Large Major Variant Comprised of Two 7 kDa Type III Afps Linked in Tandem
Authors: Wang, X. / Devries, A.L. / Cheng, C.H.
History
DepositionFeb 24, 1998Processing site: BNL
Revision 1.0Feb 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ANTIFREEZE PROTEIN RD3 TYPE III


Theoretical massNumber of molelcules
Total (without water)7,8851
Polymers7,8851
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)1 / 40AVERAGE
Representative

-
Components

#1: Protein ANTIFREEZE PROTEIN RD3 TYPE III / RD3-NL


Mass: 7885.328 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN WITH A LINKER PORTION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lycodichthys dearborni (Antarctic eel pout)
Tissue: BLOOD PLASMA / Organ: BLOOD / Variant: RD3 / Plasmid: PKK223-3UC / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P35753

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQFCOSY
121TOCSY
131NOESY
14115N-HSQC
15115N TOCSYHSQC
16115N-NOESYHSQC
17115N-HNHA
NMR detailsText: THE STRUCTURE WAS DETERMINED USING DOUBLE-RESONANCE NMR SPECTROSCOPY ON 15N-LABELED RD3-NL

-
Sample preparation

Sample conditionspH: 6.7 / Temperature: 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY5001
JEOL JNM AJEOLJNM A5002

-
Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR3.851structure solution
RefinementMethod: SA / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: AVERAGE / Conformers calculated total number: 40 / Conformers 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://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