Integral membrane protein 1906 / Protein of unknown function (DUF1461) / membrane / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Hypothetical Membrane Spanning Protein
Function and homology information
Biological species
Bacillus cereus (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å
Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
-
Details
Has ligand of interest
Y
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
ID
Density Matthews (Å3/Da)
Density % sol (%)
1
3.57
65.5
2
3.57
65.5
Crystal grow
Temperature: 293 K / Method: lipidic cubic phase / pH: 5.6 Details: 100 mM sodium citrate/HCl, pH 5.6, 40 %(v/v) polyethylene glycol (PEG) 400, 100 mM ammonium sulfate, and 200 mM sodium formate
-
Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
Serial crystal experiment
1
100
1
N
2
100
2
N
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
Diamond
I24
1
0.96862
SYNCHROTRON
SLS
X06SA
2
0.97793
Detector
Type
ID
Detector
Date
DECTRIS PILATUS3 6M
1
PIXEL
Dec 1, 2018
DECTRIS EIGER X 16M
2
PIXEL
Feb 17, 2019
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.96862
1
2
0.97793
1
Reflection
Resolution: 2.27→67.76 Å / Num. obs: 24031 / % possible obs: 91.5 % / Redundancy: 6.2 % / CC1/2: 0.96 / Rrim(I) all: 0.29 / Net I/σ(I): 3.4
Reflection shell
Resolution: 2.27→2.45 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1202 / CC1/2: 0.18 / Rrim(I) all: 1.45 / % possible all: 56.6
-
Processing
Software
Name
Version
Classification
PHENIX
1.17.1_3660
refinement
XDS
datareduction
XSCALE
datascaling
SHELXCD
phasing
BUCCANEER
modelbuilding
Refinement
Method to determine structure: SAD / Resolution: 2.33→43.32 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.65 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2873
979
4.99 %
Rwork
0.2451
18626
-
obs
0.2472
19605
64.33 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
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