- PDB-6luo: Structure of nurse shark beta-2-microglobulin -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 6luo
Title
Structure of nurse shark beta-2-microglobulin
Components
Beta-2-microglobulin
Keywords
IMMUNE SYSTEM / nurse shark / monomer beta-2-microglobulin / MHC class I
Function / homology
Function and homology information
antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein complex / immune response / extracellular region Similarity search - Function
Resolution: 2.302→33.228 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.91 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.238 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2695
639
4.961 %
Rwork
0.2376
-
-
all
0.239
-
-
obs
-
12880
93.919 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Biso mean: 42.496 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.37 Å2
0.185 Å2
0 Å2
2-
-
0.37 Å2
-0 Å2
3-
-
-
-1.2 Å2
Refinement step
Cycle: LAST / Resolution: 2.302→33.228 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1528
0
0
127
1655
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.302-2.362
50
0.325
949
X-RAY DIFFRACTION
99.7006
2.362-2.426
0.406
50
0.291
923
X-RAY DIFFRACTION
100
2.426-2.497
0.274
45
879
X-RAY DIFFRACTION
100
2.497-2.573
0.319
44
0.291
887
X-RAY DIFFRACTION
100
2.573-2.658
0.277
48
839
X-RAY DIFFRACTION
100
2.658-2.751
0.279
42
0.277
832
X-RAY DIFFRACTION
100
2.751-2.855
0.264
50
786
X-RAY DIFFRACTION
100
2.855-2.971
0.346
38
0.242
770
X-RAY DIFFRACTION
100
2.971-3.103
0.293
40
0.234
725
X-RAY DIFFRACTION
99.8695
3.103-3.254
0.242
42
0.229
703
X-RAY DIFFRACTION
99.5989
3.254-3.43
0.312
29
0.218
663
X-RAY DIFFRACTION
99.5683
3.43-3.637
0.228
26
0.209
559
X-RAY DIFFRACTION
86.0294
3.637-3.888
0.227
7
259
X-RAY DIFFRACTION
42.492
3.888-4.198
0.204
21
0.197
368
X-RAY DIFFRACTION
65.2685
4.198-4.598
0.278
28
0.177
487
X-RAY DIFFRACTION
93.4664
4.598-5.138
0.135
24
444
X-RAY DIFFRACTION
93.9759
5.138-5.928
0.221
20
0.21
421
X-RAY DIFFRACTION
99.3243
5.928-7.25
0.43
14
0.258
366
X-RAY DIFFRACTION
99.2167
+
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