Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #80 / Phage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology
Journal: J.Mol.Biol. / Year: 1997 Title: fd coat protein structure in membrane environments: structural dynamics of the loop between the hydrophobic trans-membrane helix and the amphipathic in-plane helix. Authors: Almeida, F.C. / Opella, S.J.
Mass: 5244.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: IN SDS MICELLES / Source: (natural) Enterobacteria phage fd (virus) / Genus: Inovirus / Species: Enterobacteria phage M13 / References: UniProt: P69539
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Type: 3D NOESY-TOCSY-HNHA-D2O EXCHANGE
-
Sample preparation
Sample conditions
pH: 4 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR
-
NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker DMX500
Bruker
DMX500
500
1
Bruker DMX600
Bruker
DMX600
600
2
Bruker DMX750
Bruker
DMX750
750
3
-
Processing
Software
Name
Version
Classification
X-PLOR
3.1
modelbuilding
X-PLOR
3.1
refinement
X-PLOR
3.1
phasing
NMR software
Name
Version
Developer
Classification
X-PLOR
3.1
BRUNGER
refinement
X-PLOR
structuresolution
Refinement
Method: DISTANCE GEOMETRY-SIMULATED ANNEALING / Software ordinal: 1 Details: REFINEMENT DETAILS CAN BE FOUND IN THE PAPER CITED ON JRNL RECORDS ABOVE.
NMR ensemble
Conformer selection criteria: 10 LOWEST ENERGY FOR EACH FAMILY OF STRUCTURE Conformers calculated total number: 220 / 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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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