- PDB-3oq2: Structure of a CRISPR associated protein Cas2 from Desulfovibrio ... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 3oq2
Title
Structure of a CRISPR associated protein Cas2 from Desulfovibrio vulgaris
Components
CRISPR-associated protein Cas2
Keywords
IMMUNE SYSTEM / Ferredoxin fold / CRISPR
Function / homology
Function and homology information
maintenance of CRISPR repeat elements / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / metal ion binding Similarity search - Function
CRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / Alpha-Beta Plaits - #240 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop Details: Protein solution 0.85 mM DvuCas2, reservoir solution 1 M lithium sulfate, 0.5 M ammonium sulfate and 0.1 M trisodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Method to determine structure: SAD / Resolution: 1.35→29.079 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 15.33 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.1771
2146
4.97 %
Rwork
0.1277
-
-
obs
0.1302
43191
92.58 %
all
-
46653
-
Solvent computation
Shrinkage radii: 0.4 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.873 Å2 / ksol: 0.446 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
-2.7097 Å2
-0 Å2
0.325 Å2
2-
-
-0.6712 Å2
-0 Å2
3-
-
-
1.418 Å2
Refinement step
Cycle: LAST / Resolution: 1.35→29.079 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1605
0
74
318
1997
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.006
1827
X-RAY DIFFRACTION
f_angle_d
1.119
2499
X-RAY DIFFRACTION
f_dihedral_angle_d
14.386
711
X-RAY DIFFRACTION
f_chiral_restr
0.066
252
X-RAY DIFFRACTION
f_plane_restr
0.005
321
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.35-1.3983
0.2485
180
0.1736
3313
X-RAY DIFFRACTION
75
1.3983-1.4542
0.1914
186
0.1371
3795
X-RAY DIFFRACTION
86
1.4542-1.5204
0.1799
204
0.1212
3965
X-RAY DIFFRACTION
89
1.5204-1.6006
0.1579
224
0.1067
4113
X-RAY DIFFRACTION
93
1.6006-1.7008
0.1712
192
0.1064
4189
X-RAY DIFFRACTION
96
1.7008-1.8321
0.1609
210
0.1137
4306
X-RAY DIFFRACTION
97
1.8321-2.0165
0.1754
236
0.1123
4305
X-RAY DIFFRACTION
97
2.0165-2.3082
0.1713
251
0.1114
4346
X-RAY DIFFRACTION
98
2.3082-2.9076
0.1685
236
0.1297
4364
X-RAY DIFFRACTION
98
2.9076-29.0854
0.1852
227
0.1454
4349
X-RAY DIFFRACTION
96
+
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