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- PDB-7cr8: Synechocystis Cas1-Cas2-prespacerL complex -

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Basic information

Entry
Database: PDB / ID: 7cr8
TitleSynechocystis Cas1-Cas2-prespacerL complex
Components
  • (DNA (36-MER)) x 2
  • CRISPR-associated endonuclease Cas1
  • CRISPR-associated endoribonuclease Cas2 1
KeywordsIMMUNE SYSTEM/DNA / CRISPR / adaptation / IMMUNE SYSTEM-DNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endoribonuclease activity / endodeoxyribonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
CRISPR-associated protein Cas1, cyanobacteria-type / CRISPR-associated endonuclease Cas2 / CRISPR associated protein Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain
Similarity search - Domain/homology
DNA / DNA (> 10) / CRISPR-associated endoribonuclease Cas2 1 / CRISPR-associated endonuclease Cas1
Similarity search - Component
Biological speciesSynechocystis sp. (Cyanobacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsYu, Y. / Chen, Q.
History
DepositionAug 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: CRISPR-associated endonuclease Cas1
J: CRISPR-associated endonuclease Cas1
K: CRISPR-associated endonuclease Cas1
L: CRISPR-associated endonuclease Cas1
M: CRISPR-associated endoribonuclease Cas2 1
N: CRISPR-associated endoribonuclease Cas2 1
O: DNA (36-MER)
P: DNA (36-MER)
Q: CRISPR-associated endonuclease Cas1
R: CRISPR-associated endonuclease Cas1
S: CRISPR-associated endonuclease Cas1
T: CRISPR-associated endonuclease Cas1
U: CRISPR-associated endoribonuclease Cas2 1
V: CRISPR-associated endoribonuclease Cas2 1
W: DNA (36-MER)
X: DNA (36-MER)
a: CRISPR-associated endonuclease Cas1
b: CRISPR-associated endonuclease Cas1
c: CRISPR-associated endonuclease Cas1
d: CRISPR-associated endonuclease Cas1
e: CRISPR-associated endoribonuclease Cas2 1
f: CRISPR-associated endoribonuclease Cas2 1
g: DNA (36-MER)
h: DNA (36-MER)
i: CRISPR-associated endonuclease Cas1
j: CRISPR-associated endonuclease Cas1
k: CRISPR-associated endonuclease Cas1
l: CRISPR-associated endonuclease Cas1
m: CRISPR-associated endoribonuclease Cas2 1
n: CRISPR-associated endoribonuclease Cas2 1
o: DNA (36-MER)
p: DNA (36-MER)
q: CRISPR-associated endonuclease Cas1
r: CRISPR-associated endonuclease Cas1
s: CRISPR-associated endonuclease Cas1
t: CRISPR-associated endonuclease Cas1
u: CRISPR-associated endoribonuclease Cas2 1
v: CRISPR-associated endoribonuclease Cas2 1
w: DNA (36-MER)
x: DNA (36-MER)
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: CRISPR-associated endoribonuclease Cas2 1
F: CRISPR-associated endoribonuclease Cas2 1
G: DNA (36-MER)
H: DNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)1,179,72048
Polymers1,179,72048
Non-polymers00
Water0
1
I: CRISPR-associated endonuclease Cas1
J: CRISPR-associated endonuclease Cas1
K: CRISPR-associated endonuclease Cas1
L: CRISPR-associated endonuclease Cas1
M: CRISPR-associated endoribonuclease Cas2 1
N: CRISPR-associated endoribonuclease Cas2 1
O: DNA (36-MER)
P: DNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)196,6208
Polymers196,6208
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21710 Å2
ΔGint-113 kcal/mol
Surface area76110 Å2
MethodPISA
2
Q: CRISPR-associated endonuclease Cas1
R: CRISPR-associated endonuclease Cas1
S: CRISPR-associated endonuclease Cas1
T: CRISPR-associated endonuclease Cas1
U: CRISPR-associated endoribonuclease Cas2 1
V: CRISPR-associated endoribonuclease Cas2 1
W: DNA (36-MER)
X: DNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)196,6208
Polymers196,6208
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21730 Å2
ΔGint-115 kcal/mol
Surface area76090 Å2
MethodPISA
3
a: CRISPR-associated endonuclease Cas1
b: CRISPR-associated endonuclease Cas1
c: CRISPR-associated endonuclease Cas1
d: CRISPR-associated endonuclease Cas1
e: CRISPR-associated endoribonuclease Cas2 1
f: CRISPR-associated endoribonuclease Cas2 1
g: DNA (36-MER)
h: DNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)196,6208
Polymers196,6208
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21690 Å2
ΔGint-113 kcal/mol
Surface area76250 Å2
MethodPISA
4
i: CRISPR-associated endonuclease Cas1
j: CRISPR-associated endonuclease Cas1
k: CRISPR-associated endonuclease Cas1
l: CRISPR-associated endonuclease Cas1
m: CRISPR-associated endoribonuclease Cas2 1
n: CRISPR-associated endoribonuclease Cas2 1
o: DNA (36-MER)
p: DNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)196,6208
Polymers196,6208
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21590 Å2
ΔGint-111 kcal/mol
Surface area76520 Å2
MethodPISA
5
q: CRISPR-associated endonuclease Cas1
r: CRISPR-associated endonuclease Cas1
s: CRISPR-associated endonuclease Cas1
t: CRISPR-associated endonuclease Cas1
u: CRISPR-associated endoribonuclease Cas2 1
v: CRISPR-associated endoribonuclease Cas2 1
w: DNA (36-MER)
x: DNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)196,6208
Polymers196,6208
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21770 Å2
ΔGint-119 kcal/mol
Surface area76260 Å2
MethodPISA
6
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: CRISPR-associated endoribonuclease Cas2 1
F: CRISPR-associated endoribonuclease Cas2 1
G: DNA (36-MER)
H: DNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)196,6208
Polymers196,6208
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21730 Å2
ΔGint-111 kcal/mol
Surface area76210 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)185.401, 185.401, 382.849
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201
211
221
231
241
12
22
32
42
52
62
72
82
92
102
112
122
13
23
33
43
53
63
14
24
34
44
54
64

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 2 through 26 or resid 30...A2 - 25
121(chain 'A' and (resid 2 through 26 or resid 30...A30 - 128
131(chain 'A' and (resid 2 through 26 or resid 30...A132 - 258
141(chain 'A' and (resid 2 through 26 or resid 30...A265 - 288
151(chain 'A' and (resid 2 through 26 or resid 30...A292 - 323
261(chain 'B' and (resid 2 through 26 or resid 30...B2 - 25
271(chain 'B' and (resid 2 through 26 or resid 30...B30 - 128
281(chain 'B' and (resid 2 through 26 or resid 30...B132 - 258
291(chain 'B' and (resid 2 through 26 or resid 30...B265 - 288
2101(chain 'B' and (resid 2 through 26 or resid 30...B292 - 323
3111(chain 'C' and (resid 2 through 26 or resid 30...C2 - 25
3121(chain 'C' and (resid 2 through 26 or resid 30...C30 - 128
3131(chain 'C' and (resid 2 through 26 or resid 30...C132 - 258
3141(chain 'C' and (resid 2 through 26 or resid 30...C265 - 288
3151(chain 'C' and (resid 2 through 26 or resid 30...C292 - 323
4161(chain 'D' and (resid 2 through 26 or resid 30...D2 - 25
4171(chain 'D' and (resid 2 through 26 or resid 30...D30 - 128
4181(chain 'D' and (resid 2 through 26 or resid 30...D132 - 258
4191(chain 'D' and (resid 2 through 26 or resid 30...D265 - 288
4201(chain 'D' and (resid 2 through 26 or resid 30...D292 - 323
5211(chain 'I' and (resid 2 through 26 or resid 30...I2 - 25
5221(chain 'I' and (resid 2 through 26 or resid 30...I30 - 128
5231(chain 'I' and (resid 2 through 26 or resid 30...I132 - 258
5241(chain 'I' and (resid 2 through 26 or resid 30...I265 - 288
5251(chain 'I' and (resid 2 through 26 or resid 30...I292 - 323
6261(chain 'J' and (resid 2 through 26 or resid 30...J2 - 25
6271(chain 'J' and (resid 2 through 26 or resid 30...J30 - 128
6281(chain 'J' and (resid 2 through 26 or resid 30...J132 - 258
6291(chain 'J' and (resid 2 through 26 or resid 30...J265 - 288
6301(chain 'J' and (resid 2 through 26 or resid 30...J292 - 323
7311(chain 'K' and (resid 2 through 26 or resid 30...K2 - 25
7321(chain 'K' and (resid 2 through 26 or resid 30...K30 - 128
7331(chain 'K' and (resid 2 through 26 or resid 30...K132 - 258
7341(chain 'K' and (resid 2 through 26 or resid 30...K265 - 288
7351(chain 'K' and (resid 2 through 26 or resid 30...K292 - 323
8361(chain 'L' and (resid 2 through 26 or resid 30...L2 - 25
8371(chain 'L' and (resid 2 through 26 or resid 30...L30 - 128
8381(chain 'L' and (resid 2 through 26 or resid 30...L132 - 258
8391(chain 'L' and (resid 2 through 26 or resid 30...L265 - 288
8401(chain 'L' and (resid 2 through 26 or resid 30...L292 - 323
9411(chain 'Q' and (resid 2 through 26 or resid 30...Q2 - 25
9421(chain 'Q' and (resid 2 through 26 or resid 30...Q30 - 128
9431(chain 'Q' and (resid 2 through 26 or resid 30...Q132 - 258
9441(chain 'Q' and (resid 2 through 26 or resid 30...Q265 - 288
9451(chain 'Q' and (resid 2 through 26 or resid 30...Q292 - 323
10461(chain 'R' and (resid 2 through 26 or resid 30...R2 - 25
10471(chain 'R' and (resid 2 through 26 or resid 30...R30 - 128
10481(chain 'R' and (resid 2 through 26 or resid 30...R132 - 258
10491(chain 'R' and (resid 2 through 26 or resid 30...R265 - 288
10501(chain 'R' and (resid 2 through 26 or resid 30...R292 - 323
11511(chain 'S' and (resid 2 through 26 or resid 30...S2 - 25
11521(chain 'S' and (resid 2 through 26 or resid 30...S30 - 128
11531(chain 'S' and (resid 2 through 26 or resid 30...S132 - 258
11541(chain 'S' and (resid 2 through 26 or resid 30...S265 - 288
11551(chain 'S' and (resid 2 through 26 or resid 30...S292 - 323
12561(chain 'T' and (resid 2 through 26 or resid 30...T2 - 25
12571(chain 'T' and (resid 2 through 26 or resid 30...T30 - 128
12581(chain 'T' and (resid 2 through 26 or resid 30...T132 - 258
12591(chain 'T' and (resid 2 through 26 or resid 30...T265 - 288
12601(chain 'T' and (resid 2 through 26 or resid 30...T292 - 323
13611(chain 'a' and (resid 2 through 26 or resid 30...a2 - 25
13621(chain 'a' and (resid 2 through 26 or resid 30...a30 - 128
13631(chain 'a' and (resid 2 through 26 or resid 30...a132 - 258
13641(chain 'a' and (resid 2 through 26 or resid 30...a265 - 288
13651(chain 'a' and (resid 2 through 26 or resid 30...a292 - 323
14661(chain 'b' and (resid 2 through 26 or resid 30...b2 - 25
14671(chain 'b' and (resid 2 through 26 or resid 30...b30 - 128
14681(chain 'b' and (resid 2 through 26 or resid 30...b132 - 258
14691(chain 'b' and (resid 2 through 26 or resid 30...b265 - 288
14701(chain 'b' and (resid 2 through 26 or resid 30...b292 - 323
15711(chain 'c' and (resid 2 through 26 or resid 30...c2 - 25
15721(chain 'c' and (resid 2 through 26 or resid 30...c30 - 128
15731(chain 'c' and (resid 2 through 26 or resid 30...c132 - 258
15741(chain 'c' and (resid 2 through 26 or resid 30...c265 - 288
15751(chain 'c' and (resid 2 through 26 or resid 30...c292 - 323
16761(chain 'd' and (resid 2 through 26 or resid 30...d2 - 25
16771(chain 'd' and (resid 2 through 26 or resid 30...d30 - 128
16781(chain 'd' and (resid 2 through 26 or resid 30...d132 - 258
16791(chain 'd' and (resid 2 through 26 or resid 30...d265 - 288
16801(chain 'd' and (resid 2 through 26 or resid 30...d292 - 323
17811(chain 'i' and (resid 2 through 26 or resid 30...i2 - 25
17821(chain 'i' and (resid 2 through 26 or resid 30...i30 - 128
17831(chain 'i' and (resid 2 through 26 or resid 30...i132 - 258
17841(chain 'i' and (resid 2 through 26 or resid 30...i265 - 288
17851(chain 'i' and (resid 2 through 26 or resid 30...i292 - 323
18861(chain 'j' and (resid 2 through 26 or resid 30...j2 - 25
18871(chain 'j' and (resid 2 through 26 or resid 30...j30 - 128
18881(chain 'j' and (resid 2 through 26 or resid 30...j132 - 258
18891(chain 'j' and (resid 2 through 26 or resid 30...j265 - 288
18901(chain 'j' and (resid 2 through 26 or resid 30...j292 - 323
19911(chain 'k' and (resid 2 through 26 or resid 30...k2 - 25
19921(chain 'k' and (resid 2 through 26 or resid 30...k30 - 128
19931(chain 'k' and (resid 2 through 26 or resid 30...k132 - 258
19941(chain 'k' and (resid 2 through 26 or resid 30...k265 - 288
19951(chain 'k' and (resid 2 through 26 or resid 30...k292 - 323
20961(chain 'l' and (resid 2 through 26 or resid 30...l2 - 25
20971(chain 'l' and (resid 2 through 26 or resid 30...l30 - 128
20981(chain 'l' and (resid 2 through 26 or resid 30...l132 - 258
20991(chain 'l' and (resid 2 through 26 or resid 30...l265 - 288
201001(chain 'l' and (resid 2 through 26 or resid 30...l292 - 323
211011(chain 'q' and (resid 2 through 26 or resid 30...q2 - 25
211021(chain 'q' and (resid 2 through 26 or resid 30...q30 - 128
211031(chain 'q' and (resid 2 through 26 or resid 30...q132 - 258
211041(chain 'q' and (resid 2 through 26 or resid 30...q265 - 288
211051(chain 'q' and (resid 2 through 26 or resid 30...q292 - 323
221061(chain 'r' and (resid 2 through 26 or resid 30...r2 - 25
221071(chain 'r' and (resid 2 through 26 or resid 30...r30 - 128
221081(chain 'r' and (resid 2 through 26 or resid 30...r132 - 258
221091(chain 'r' and (resid 2 through 26 or resid 30...r265 - 288
221101(chain 'r' and (resid 2 through 26 or resid 30...r292 - 323
231111(chain 's' and (resid 2 through 26 or resid 30...s2 - 25
231121(chain 's' and (resid 2 through 26 or resid 30...s30 - 128
231131(chain 's' and (resid 2 through 26 or resid 30...s132 - 258
231141(chain 's' and (resid 2 through 26 or resid 30...s265 - 288
231151(chain 's' and (resid 2 through 26 or resid 30...s292 - 323
241161(chain 't' and (resid 2 through 26 or resid 30...t2 - 25
241171(chain 't' and (resid 2 through 26 or resid 30...t30 - 128
241181(chain 't' and (resid 2 through 26 or resid 30...t132 - 258
241191(chain 't' and (resid 2 through 26 or resid 30...t265 - 288
241201(chain 't' and (resid 2 through 26 or resid 30...t292 - 323
11212(chain 'E' and resid 2 through 93)E2 - 92
21222(chain 'F' and resid 2 through 93)F2 - 92
31232(chain 'M' and resid 2 through 93)M2 - 92
41242(chain 'N' and resid 2 through 93)N2 - 92
51252(chain 'U' and resid 2 through 93)U2 - 92
61262(chain 'V' and resid 2 through 93)V2 - 92
71272(chain 'e' and resid 2 through 93)e2 - 92
81282(chain 'f' and resid 2 through 93)f2 - 92
91292(chain 'm' and resid 2 through 93)m2 - 92
101302(chain 'n' and resid 2 through 93)n2 - 92
111312(chain 'u' and resid 2 through 93)u2 - 92
121322(chain 'v' and resid 2 through 93)v2 - 92
11333(chain 'G' and (resid 6 through 28 or resid 31 through 33))G6 - 28
11343(chain 'G' and (resid 6 through 28 or resid 31 through 33))G31 - 33
21353(chain 'O' and (resid 6 through 28 or resid 31 through 33))O6 - 28
21363(chain 'O' and (resid 6 through 28 or resid 31 through 33))O31 - 33
31373(chain 'W' and (resid 6 through 28 or resid 31 through 33))W6 - 28
31383(chain 'W' and (resid 6 through 28 or resid 31 through 33))W31 - 33
41393(chain 'g' and (resid 6 through 28 or resid 31 through 33))g6 - 28
41403(chain 'g' and (resid 6 through 28 or resid 31 through 33))g31 - 33
51413(chain 'o' and (resid 6 through 28 or resid 31 through 33))o6 - 28
51423(chain 'o' and (resid 6 through 28 or resid 31 through 33))o31 - 33
61433(chain 'w' and (resid 6 through 28 or resid 31 through 33))w6 - 28
61443(chain 'w' and (resid 6 through 28 or resid 31 through 33))w31 - 33
11454(chain 'H' and (resid 8 through 29 or resid 32 through 34))H8 - 29
11464(chain 'H' and (resid 8 through 29 or resid 32 through 34))H32 - 34
21474(chain 'P' and (resid 8 through 29 or resid 32 through 34))P8 - 29
21484(chain 'P' and (resid 8 through 29 or resid 32 through 34))P32 - 34
31494(chain 'X' and (resid 8 through 29 or resid 32 through 34))X8 - 29
31504(chain 'X' and (resid 8 through 29 or resid 32 through 34))X32 - 34
41514(chain 'h' and (resid 8 through 29 or resid 32 through 34))h8 - 29
41524(chain 'h' and (resid 8 through 29 or resid 32 through 34))h32 - 34
51534(chain 'p' and (resid 8 through 29 or resid 32 through 34))p8 - 29
51544(chain 'p' and (resid 8 through 29 or resid 32 through 34))p32 - 34
61554(chain 'x' and (resid 8 through 29 or resid 32 through 34))x8 - 29
61564(chain 'x' and (resid 8 through 29 or resid 32 through 34))x32 - 34

NCS ensembles:
ID
1
2
3
4

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Components

#1: Protein ...
CRISPR-associated endonuclease Cas1


Mass: 37811.238 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (Cyanobacteria)
Strain: PCC 6803 / Kazusa / Gene: cas1, slr7016 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6ZEI2, Hydrolases; Acting on ester bonds
#2: Protein
CRISPR-associated endoribonuclease Cas2 1


Mass: 11656.425 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (Cyanobacteria)
Strain: PCC 6803 / Kazusa / Gene: cas2-1, ssr7017 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6ZEI1, Hydrolases; Acting on ester bonds
#3: DNA chain
DNA (36-MER)


Mass: 11004.026 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain
DNA (36-MER)


Mass: 11058.110 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% MPD, 0.1 M imidazole pH 6.5, 0.2 M (NH4)2SO4, 10% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.69→50 Å / Num. obs: 157305 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 130.45 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.68
Reflection shellResolution: 3.69→3.92 Å / Num. unique obs: 25305 / CC1/2: 0.838

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CR6
Resolution: 3.7→47.56 Å / SU ML: 0.7752 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 42.3464
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3409 1566 1 %
Rwork0.2955 155399 -
Obs0.2959 156965 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 147.92 Å2
Refinement stepCycle: LAST / Resolution: 3.7→47.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms71378 7242 0 0 78620
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004181050
X-RAY DIFFRACTIONf_angle_d0.9485111106
X-RAY DIFFRACTIONf_chiral_restr0.043412313
X-RAY DIFFRACTIONf_plane_restr0.005913021
X-RAY DIFFRACTIONf_dihedral_angle_d10.865947316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
3.7-3.820.46921420.394914089X-RAY DIFFRACTION99.65
3.82-3.950.49261430.375414153X-RAY DIFFRACTION99.71
3.95-4.110.36861420.348714093X-RAY DIFFRACTION99.84
4.11-4.30.36151420.340414211X-RAY DIFFRACTION99.89
4.3-4.520.36121430.310414156X-RAY DIFFRACTION99.88
4.52-4.810.331410.296414064X-RAY DIFFRACTION99.96
4.81-5.180.36461440.30714187X-RAY DIFFRACTION99.92
5.18-5.70.40891420.320514118X-RAY DIFFRACTION99.99
5.7-6.520.34821430.33214150X-RAY DIFFRACTION99.97
6.52-8.210.37541430.296314173X-RAY DIFFRACTION99.94
8.21-47.560.23011410.214714005X-RAY DIFFRACTION98.85

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

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Yorodumi

Thousand views of thousand structures

  • 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.

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

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