Name: sapA / Type: protein / Description: saposin-a / Formula weight: 9.084 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: P07602 Sequence:
SMSLPCDICK DVVTAAGDML KDNATEEEIL VYLEKTCDWL PKPNMSASCK EIVDSYLPVI LDIIKGEMSR PGEVCSALNL CES
Entity #783
Name: DOPC / Type: other / Description: 1,2-dioleoyl-sn-glycero-3-phosphocholine / Formula weight: 0.78 / Source: Synthetic compound
-
Experimental information
Beam
Instrument name: PETRA III P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3.1 mm
Detector
Name: Pilatus 2M
Scan
Title: sapAdopc / Measurement date: Dec 15, 2016 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /
Min
Max
Q
0.0195
5.0075
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 1169 /
Min
Max
Q
0.104419
3.30551
P(R) point
1
1169
R
0
11.5
Result
Type of curve: extrapolated
Experimental
Experimental error
Porod
Porod error
MW
33 kDa
5
56 kDa
6
Volume
-
-
96 nm3
10
P(R)
P(R) error
Guinier
Guinier error
Forward scattering, I0
39720
40
40271
55
Radius of gyration, Rg
4 nm
0.1
4.1 nm
0.1
Min
Max
Error
D
-
11.5
0.5
Guinier point
32
105
-
+
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