[English] 日本語
Yorodumi
- PDB-7yq7: Crystal structure of photosystem II expressing psbA3 gene only -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yq7
TitleCrystal structure of photosystem II expressing psbA3 gene only
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 17
  • Cytochrome c-550
KeywordsPHOTOSYNTHESIS / ELECTRON TRANSPORT
Function / homology
Function and homology information


photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II ...photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / extrinsic component of membrane / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthesis / respiratory electron transport chain / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily ...Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbM / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / (3R)-beta,beta-caroten-3-ol / Chem-SQD / Unknown ligand / Photosystem II extrinsic protein V / Photosystem II extrinsic protein O / Photosystem II reaction center protein J / Photosystem II D2 protein / Photosystem II reaction center protein M / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Cytochrome b559 subunit alpha / Photosystem II reaction center protein T / Photosystem II CP47 reaction center protein / Photosystem II protein D1 3 / Photosystem II reaction center protein H / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein I / Photosystem II reaction center protein Y / Photosystem II reaction center protein K / Photosystem II extrinsic protein U / Photosystem II reaction center protein X
Similarity search - Component
Biological speciesThermosynechococcus vestitus BP-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNakajima, Y. / Suga, M. / Shen, J.R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H03226 Japan
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Crystal structures of photosystem II from a cyanobacterium expressing psbA 2 in comparison to psbA 3 reveal differences in the D1 subunit.
Authors: Nakajima, Y. / Ugai-Amo, N. / Tone, N. / Nakagawa, A. / Iwai, M. / Ikeuchi, M. / Sugiura, M. / Suga, M. / Shen, J.R.
History
DepositionAug 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Photosystem II protein D1 3
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Photosystem II manganese-stabilizing polypeptide
T: Photosystem II reaction center protein T
U: Photosystem II 12 kDa extrinsic protein
V: Cytochrome c-550
X: Photosystem II reaction center X protein
Y: Photosystem II reaction center protein Ycf12
Z: Photosystem II reaction center protein Z
a: Photosystem II protein D1 3
b: Photosystem II CP47 reaction center protein
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
j: Photosystem II reaction center protein J
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
o: Photosystem II manganese-stabilizing polypeptide
t: Photosystem II reaction center protein T
u: Photosystem II 12 kDa extrinsic protein
v: Cytochrome c-550
x: Photosystem II reaction center X protein
y: Photosystem II reaction center protein Ycf12
z: Photosystem II reaction center protein Z
R: Photosystem II protein Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)788,654401
Polymers630,09239
Non-polymers158,562362
Water59,2693290
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.804, 228.456, 286.852
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 11 through 220 or resid 222 through 344 or resid 410))
21(chain a and (resid 11 through 220 or resid 222 through 344 or resid 410))
12(chain B and (resid 2 through 13 or resid 15...
22(chain b and (resid 2 through 13 or resid 15...
13(chain C and (resid 24 through 144 or resid 146...
23(chain c and (resid 24 through 144 or resid 146...
14(chain D and (resid 12 through 294 or resid 296...
24(chain d and ((resid 12 and (name N or name...
15(chain E and (resid 6 through 53 or resid 55...
25(chain e and (resid 6 through 53 or resid 55...
16(chain F and (resid 14 through 45 or resid 101))
26(chain f and (resid 14 through 45 or resid 101))
17(chain H and (resid 2 or resid 4 through 65 or resid 103))
27(chain h and (resid 2 or resid 4 through 65...
18(chain I and (resid 1 through 101 or (resid 102...
28(chain i and (resid 1 through 32 or (resid 33...
19(chain J and (resid 4 through 40 or resid 101 through 103))
29(chain j and ((resid 4 and (name N or name...
110chain K
210(chain k and (resid 10 through 46 or resid 101 through 102))
111(chain L and (resid 2 through 23 or resid 25 through 37 or resid 101))
211(chain l and ((resid 2 and (name N or name...
112(chain M and (resid 1 through 15 or resid 17 through 102))
212(chain m and (resid 1 through 15 or resid 17...
113(chain O and (resid 4 through 26 or (resid 27...
213(chain o and (resid 4 through 73 or resid 75...
114(chain T and (resid 1 through 30 or resid 101))
214(chain t and (resid 1 through 30 or resid 101))
115(chain U and resid 8 through 104)
215(chain u and (resid 8 through 85 or (resid 86...
116(chain V and (resid 1 through 13 or resid 15...
216(chain v and (resid 1 through 13 or resid 15 through 34 or resid 36 through 137 or resid 201))
117(chain X and (resid 2 through 14 or resid 16...
217(chain x and (resid 2 through 14 or resid 16 through 39))
118(chain Y and ((resid 18 through 20 and (name N...
218(chain y and (resid 18 through 42 or (resid 43...
119(chain Z and ((resid 1 through 4 and (name N...
219(chain z and ((resid 1 through 4 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 11 through 220 or resid 222 through 344 or resid 410))A11 - 220
121(chain A and (resid 11 through 220 or resid 222 through 344 or resid 410))A222 - 344
131(chain A and (resid 11 through 220 or resid 222 through 344 or resid 410))A410
211(chain a and (resid 11 through 220 or resid 222 through 344 or resid 410))a11 - 220
221(chain a and (resid 11 through 220 or resid 222 through 344 or resid 410))a222 - 344
231(chain a and (resid 11 through 220 or resid 222 through 344 or resid 410))a410
112(chain B and (resid 2 through 13 or resid 15...B2 - 13
122(chain B and (resid 2 through 13 or resid 15...B15 - 35
132(chain B and (resid 2 through 13 or resid 15...B37 - 222
142(chain B and (resid 2 through 13 or resid 15...B224 - 238
152(chain B and (resid 2 through 13 or resid 15...B240 - 284
162(chain B and (resid 2 through 13 or resid 15...B286
172(chain B and (resid 2 through 13 or resid 15...B348 - 397
182(chain B and (resid 2 through 13 or resid 15...B399 - 430
192(chain B and (resid 2 through 13 or resid 15...B432 - 483
1102(chain B and (resid 2 through 13 or resid 15...B2 - 1027
1112(chain B and (resid 2 through 13 or resid 15...B2 - 1027
1122(chain B and (resid 2 through 13 or resid 15...B2 - 1027
1132(chain B and (resid 2 through 13 or resid 15...B2 - 1027
1142(chain B and (resid 2 through 13 or resid 15...B2 - 1027
212(chain b and (resid 2 through 13 or resid 15...b2 - 13
222(chain b and (resid 2 through 13 or resid 15...b15 - 35
232(chain b and (resid 2 through 13 or resid 15...b37 - 222
242(chain b and (resid 2 through 13 or resid 15...b224 - 226
252(chain b and (resid 2 through 13 or resid 15...b2 - 505
262(chain b and (resid 2 through 13 or resid 15...b2 - 505
272(chain b and (resid 2 through 13 or resid 15...b2 - 505
282(chain b and (resid 2 through 13 or resid 15...b2 - 505
292(chain b and (resid 2 through 13 or resid 15...b2 - 505
2102(chain b and (resid 2 through 13 or resid 15...b2 - 505
2112(chain b and (resid 2 through 13 or resid 15...b2 - 505
113(chain C and (resid 24 through 144 or resid 146...C24 - 144
123(chain C and (resid 24 through 144 or resid 146...C146 - 206
133(chain C and (resid 24 through 144 or resid 146...C207
143(chain C and (resid 24 through 144 or resid 146...C24 - 1004
153(chain C and (resid 24 through 144 or resid 146...C24 - 1004
163(chain C and (resid 24 through 144 or resid 146...C24 - 1004
173(chain C and (resid 24 through 144 or resid 146...C24 - 1004
213(chain c and (resid 24 through 144 or resid 146...c24 - 144
223(chain c and (resid 24 through 144 or resid 146...c146 - 212
233(chain c and (resid 24 through 144 or resid 146...c214 - 377
243(chain c and (resid 24 through 144 or resid 146...c379 - 415
253(chain c and (resid 24 through 144 or resid 146...c417 - 470
263(chain c and (resid 24 through 144 or resid 146...c472 - 473
273(chain c and (resid 24 through 144 or resid 146...c917
283(chain c and (resid 24 through 144 or resid 146...c19 - 473
293(chain c and (resid 24 through 144 or resid 146...c19 - 473
2103(chain c and (resid 24 through 144 or resid 146...c19 - 473
2113(chain c and (resid 24 through 144 or resid 146...c19 - 473
2123(chain c and (resid 24 through 144 or resid 146...c19 - 473
2133(chain c and (resid 24 through 144 or resid 146...c19 - 473
2143(chain c and (resid 24 through 144 or resid 146...c19 - 473
114(chain D and (resid 12 through 294 or resid 296...D12 - 294
124(chain D and (resid 12 through 294 or resid 296...D296 - 352
134(chain D and (resid 12 through 294 or resid 296...D402 - 405
144(chain D and (resid 12 through 294 or resid 296...D408
154(chain D and (resid 12 through 294 or resid 296...D12 - 418
164(chain D and (resid 12 through 294 or resid 296...D12 - 418
174(chain D and (resid 12 through 294 or resid 296...D12 - 418
184(chain D and (resid 12 through 294 or resid 296...D12 - 418
194(chain D and (resid 12 through 294 or resid 296...D12 - 418
1104(chain D and (resid 12 through 294 or resid 296...D12 - 418
1114(chain D and (resid 12 through 294 or resid 296...D12 - 418
1124(chain D and (resid 12 through 294 or resid 296...D12 - 418
1134(chain D and (resid 12 through 294 or resid 296...D12 - 418
1144(chain D and (resid 12 through 294 or resid 296...D12 - 418
1154(chain D and (resid 12 through 294 or resid 296...D12 - 418
1164(chain D and (resid 12 through 294 or resid 296...D12 - 418
1174(chain D and (resid 12 through 294 or resid 296...D12 - 418
1184(chain D and (resid 12 through 294 or resid 296...D12 - 418
1194(chain D and (resid 12 through 294 or resid 296...D12 - 418
1204(chain D and (resid 12 through 294 or resid 296...D12 - 418
1214(chain D and (resid 12 through 294 or resid 296...D12 - 418
1224(chain D and (resid 12 through 294 or resid 296...D12 - 418
1234(chain D and (resid 12 through 294 or resid 296...D12 - 418
1244(chain D and (resid 12 through 294 or resid 296...D12 - 418
1254(chain D and (resid 12 through 294 or resid 296...D12 - 418
1264(chain D and (resid 12 through 294 or resid 296...D12 - 418
1274(chain D and (resid 12 through 294 or resid 296...D12 - 418
1284(chain D and (resid 12 through 294 or resid 296...D12 - 418
1294(chain D and (resid 12 through 294 or resid 296...D12 - 418
1304(chain D and (resid 12 through 294 or resid 296...D12 - 418
1314(chain D and (resid 12 through 294 or resid 296...D12 - 418
1324(chain D and (resid 12 through 294 or resid 296...D12 - 418
1334(chain D and (resid 12 through 294 or resid 296...D12 - 418
1344(chain D and (resid 12 through 294 or resid 296...D12 - 418
1354(chain D and (resid 12 through 294 or resid 296...D12 - 418
1364(chain D and (resid 12 through 294 or resid 296...D12 - 418
1374(chain D and (resid 12 through 294 or resid 296...D12 - 418
1384(chain D and (resid 12 through 294 or resid 296...D12 - 418
1394(chain D and (resid 12 through 294 or resid 296...D12 - 418
1404(chain D and (resid 12 through 294 or resid 296...D12 - 418
1414(chain D and (resid 12 through 294 or resid 296...D12 - 418
1424(chain D and (resid 12 through 294 or resid 296...D12 - 418
1434(chain D and (resid 12 through 294 or resid 296...D12 - 418
1444(chain D and (resid 12 through 294 or resid 296...D12 - 418
1454(chain D and (resid 12 through 294 or resid 296...D12 - 418
214(chain d and ((resid 12 and (name N or name...d12
224(chain d and ((resid 12 and (name N or name...d11 - 352
234(chain d and ((resid 12 and (name N or name...d11 - 352
244(chain d and ((resid 12 and (name N or name...d11 - 352
254(chain d and ((resid 12 and (name N or name...d11 - 352
115(chain E and (resid 6 through 53 or resid 55...E6 - 53
125(chain E and (resid 6 through 53 or resid 55...E55 - 58
135(chain E and (resid 6 through 53 or resid 55...E59 - 60
145(chain E and (resid 6 through 53 or resid 55...E4 - 103
155(chain E and (resid 6 through 53 or resid 55...E4 - 103
165(chain E and (resid 6 through 53 or resid 55...E4 - 103
175(chain E and (resid 6 through 53 or resid 55...E4 - 103
215(chain e and (resid 6 through 53 or resid 55...e6 - 53
225(chain e and (resid 6 through 53 or resid 55...e55 - 61
235(chain e and (resid 6 through 53 or resid 55...e63 - 73
245(chain e and (resid 6 through 53 or resid 55...e74
255(chain e and (resid 6 through 53 or resid 55...e6 - 84
265(chain e and (resid 6 through 53 or resid 55...e6 - 84
275(chain e and (resid 6 through 53 or resid 55...e6 - 84
285(chain e and (resid 6 through 53 or resid 55...e6 - 84
116(chain F and (resid 14 through 45 or resid 101))F0
216(chain f and (resid 14 through 45 or resid 101))f0
117(chain H and (resid 2 or resid 4 through 65 or resid 103))H2
127(chain H and (resid 2 or resid 4 through 65 or resid 103))H4 - 65
137(chain H and (resid 2 or resid 4 through 65 or resid 103))H103
217(chain h and (resid 2 or resid 4 through 65...h2
227(chain h and (resid 2 or resid 4 through 65...h4 - 65
237(chain h and (resid 2 or resid 4 through 65...h106
247(chain h and (resid 2 or resid 4 through 65...h2 - 66
257(chain h and (resid 2 or resid 4 through 65...h2 - 66
267(chain h and (resid 2 or resid 4 through 65...h2 - 66
277(chain h and (resid 2 or resid 4 through 65...h2 - 66
287(chain h and (resid 2 or resid 4 through 65...h2 - 66
297(chain h and (resid 2 or resid 4 through 65...h2 - 66
2107(chain h and (resid 2 or resid 4 through 65...h2 - 66
118(chain I and (resid 1 through 101 or (resid 102...I0
218(chain i and (resid 1 through 32 or (resid 33...i1 - 32
228(chain i and (resid 1 through 32 or (resid 33...i33 - 36
238(chain i and (resid 1 through 32 or (resid 33...i1 - 37
248(chain i and (resid 1 through 32 or (resid 33...i1 - 37
258(chain i and (resid 1 through 32 or (resid 33...i1 - 37
268(chain i and (resid 1 through 32 or (resid 33...i1 - 37
119(chain J and (resid 4 through 40 or resid 101 through 103))J4 - 40
129(chain J and (resid 4 through 40 or resid 101 through 103))J101 - 103
219(chain j and ((resid 4 and (name N or name...j4
229(chain j and ((resid 4 and (name N or name...j3 - 40
239(chain j and ((resid 4 and (name N or name...j3 - 40
249(chain j and ((resid 4 and (name N or name...j3 - 40
259(chain j and ((resid 4 and (name N or name...j3 - 40
1110chain KK10 - 102
2110(chain k and (resid 10 through 46 or resid 101 through 102))k10 - 46
2210(chain k and (resid 10 through 46 or resid 101 through 102))k101 - 102
1111(chain L and (resid 2 through 23 or resid 25 through 37 or resid 101))L2 - 23
1211(chain L and (resid 2 through 23 or resid 25 through 37 or resid 101))L25 - 37
1311(chain L and (resid 2 through 23 or resid 25 through 37 or resid 101))L101
2111(chain l and ((resid 2 and (name N or name...l2
2211(chain l and ((resid 2 and (name N or name...l2 - 37
2311(chain l and ((resid 2 and (name N or name...l2 - 37
2411(chain l and ((resid 2 and (name N or name...l2 - 37
2511(chain l and ((resid 2 and (name N or name...l2 - 37
1112(chain M and (resid 1 through 15 or resid 17 through 102))M1 - 15
1212(chain M and (resid 1 through 15 or resid 17 through 102))M17 - 102
2112(chain m and (resid 1 through 15 or resid 17...m1 - 15
2212(chain m and (resid 1 through 15 or resid 17...m17 - 32
2312(chain m and (resid 1 through 15 or resid 17...m33 - 34
2412(chain m and (resid 1 through 15 or resid 17...m1 - 34
2512(chain m and (resid 1 through 15 or resid 17...m1 - 34
2612(chain m and (resid 1 through 15 or resid 17...m1 - 34
2712(chain m and (resid 1 through 15 or resid 17...m1 - 34
1113(chain O and (resid 4 through 26 or (resid 27...O4 - 26
1213(chain O and (resid 4 through 26 or (resid 27...O27
1313(chain O and (resid 4 through 26 or (resid 27...O4 - 246
1413(chain O and (resid 4 through 26 or (resid 27...O4 - 246
1513(chain O and (resid 4 through 26 or (resid 27...O4 - 246
1613(chain O and (resid 4 through 26 or (resid 27...O4 - 246
2113(chain o and (resid 4 through 73 or resid 75...o4 - 73
2213(chain o and (resid 4 through 73 or resid 75...o75 - 97
2313(chain o and (resid 4 through 73 or resid 75...o98
2413(chain o and (resid 4 through 73 or resid 75...o4 - 246
2513(chain o and (resid 4 through 73 or resid 75...o4 - 246
2613(chain o and (resid 4 through 73 or resid 75...o4 - 246
1114(chain T and (resid 1 through 30 or resid 101))T0
2114(chain t and (resid 1 through 30 or resid 101))t0
1115(chain U and resid 8 through 104)U8 - 104
2115(chain u and (resid 8 through 85 or (resid 86...u8 - 85
2215(chain u and (resid 8 through 85 or (resid 86...u86
2315(chain u and (resid 8 through 85 or (resid 86...u8 - 104
2415(chain u and (resid 8 through 85 or (resid 86...u8 - 104
2515(chain u and (resid 8 through 85 or (resid 86...u8 - 104
2615(chain u and (resid 8 through 85 or (resid 86...u8 - 104
1116(chain V and (resid 1 through 13 or resid 15...V1 - 13
1216(chain V and (resid 1 through 13 or resid 15...V15 - 23
1316(chain V and (resid 1 through 13 or resid 15...V24
1416(chain V and (resid 1 through 13 or resid 15...V1 - 137
1516(chain V and (resid 1 through 13 or resid 15...V1 - 137
1616(chain V and (resid 1 through 13 or resid 15...V1 - 137
1716(chain V and (resid 1 through 13 or resid 15...V1 - 137
2116(chain v and (resid 1 through 13 or resid 15 through 34 or resid 36 through 137 or resid 201))v1 - 13
2216(chain v and (resid 1 through 13 or resid 15 through 34 or resid 36 through 137 or resid 201))v15 - 34
2316(chain v and (resid 1 through 13 or resid 15 through 34 or resid 36 through 137 or resid 201))v36 - 137
2416(chain v and (resid 1 through 13 or resid 15 through 34 or resid 36 through 137 or resid 201))v201
1117(chain X and (resid 2 through 14 or resid 16...X2 - 14
1217(chain X and (resid 2 through 14 or resid 16...X16 - 37
1317(chain X and (resid 2 through 14 or resid 16...X38
1417(chain X and (resid 2 through 14 or resid 16...X2 - 41
1517(chain X and (resid 2 through 14 or resid 16...X2 - 41
1617(chain X and (resid 2 through 14 or resid 16...X2 - 41
1717(chain X and (resid 2 through 14 or resid 16...X2 - 41
2117(chain x and (resid 2 through 14 or resid 16 through 39))x2 - 14
2217(chain x and (resid 2 through 14 or resid 16 through 39))x16 - 39
1118(chain Y and ((resid 18 through 20 and (name N...Y18 - 20
1218(chain Y and ((resid 18 through 20 and (name N...Y18 - 46
1318(chain Y and ((resid 18 through 20 and (name N...Y18 - 46
1418(chain Y and ((resid 18 through 20 and (name N...Y18 - 46
1518(chain Y and ((resid 18 through 20 and (name N...Y18 - 46
2118(chain y and (resid 18 through 42 or (resid 43...y18 - 42
2218(chain y and (resid 18 through 42 or (resid 43...y43
2318(chain y and (resid 18 through 42 or (resid 43...y17 - 46
2418(chain y and (resid 18 through 42 or (resid 43...y17 - 46
2518(chain y and (resid 18 through 42 or (resid 43...y17 - 46
2618(chain y and (resid 18 through 42 or (resid 43...y17 - 46
1119(chain Z and ((resid 1 through 4 and (name N...Z1 - 4
1219(chain Z and ((resid 1 through 4 and (name N...Z1 - 62
1319(chain Z and ((resid 1 through 4 and (name N...Z1 - 62
1419(chain Z and ((resid 1 through 4 and (name N...Z1 - 62
1519(chain Z and ((resid 1 through 4 and (name N...Z1 - 62
2119(chain z and ((resid 1 through 4 and (name N...z1 - 4
2219(chain z and ((resid 1 through 4 and (name N...z1 - 101
2319(chain z and ((resid 1 through 4 and (name N...z1 - 101
2419(chain z and ((resid 1 through 4 and (name N...z1 - 101
2519(chain z and ((resid 1 through 4 and (name N...z1 - 101

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19

-
Components

-
Photosystem II ... , 17 types, 33 molecules AaBbCcDdHhIiJjKkLlMmOoTtUuXxYy...

#1: Protein Photosystem II protein D1 3 / / PSII D1 protein 3 / Photosystem II Q(B) protein 3


Mass: 39780.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIV4, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / / PSII 47 kDa protein / Protein CP-47


Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIQ1
#3: Protein Photosystem II CP43 reaction center protein / / PSII 43 kDa protein / Protein CP-43


Mass: 50287.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIF8
#4: Protein Photosystem II D2 protein / / PSII D2 protein / Photosystem II Q(A) protein


Mass: 39388.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8CM25, photosystem II
#7: Protein Photosystem II reaction center protein H / / PSII-H


Mass: 7358.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DJ43
#8: Protein/peptide Photosystem II reaction center protein I / / PSII-I / PSII 4.4 kDa protein


Mass: 4438.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DJZ6
#9: Protein/peptide Photosystem II reaction center protein J / / PSII-J


Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P59087
#10: Protein/peptide Photosystem II reaction center protein K / / PSII-K


Mass: 5028.083 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q9F1K9
#11: Protein/peptide Photosystem II reaction center protein L / / PSII-L


Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIN8
#12: Protein/peptide Photosystem II reaction center protein M / / PSII-M


Mass: 4009.682 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DHA7
#13: Protein Photosystem II manganese-stabilizing polypeptide / / MSP


Mass: 29637.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A431
#14: Protein/peptide Photosystem II reaction center protein T / / PSII-T / PSII-Tc


Mass: 3906.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIQ0
#15: Protein Photosystem II 12 kDa extrinsic protein / / PS II complex 12 kDa extrinsic protein / PSII-U


Mass: 15030.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q9F1L5
#17: Protein/peptide Photosystem II reaction center X protein /


Mass: 4322.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q9F1R6
#18: Protein/peptide Photosystem II reaction center protein Ycf12 /


Mass: 5039.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DJI1
#19: Protein Photosystem II reaction center protein Z / / PSII-Z


Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DHJ2
#20: Protein/peptide Photosystem II protein Y /


Mass: 4590.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DKM3

-
Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf

#5: Protein Cytochrome b559 subunit alpha / / PSII reaction center subunit V


Mass: 9580.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIP0
#6: Protein/peptide Cytochrome b559 subunit beta / / PSII reaction center subunit VI


Mass: 5067.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIN9

-
Protein , 1 types, 2 molecules Vv

#16: Protein Cytochrome c-550 / Cytochrome c-549 / Cytochrome c550 / Low-potential cytochrome c


Mass: 18046.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A386

-
Sugars , 3 types, 45 molecules

#32: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#36: Sugar
ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside / HEPTYL 1-THIOHEXOPYRANOSIDE / heptyl 1-thio-beta-D-glucoside / heptyl 1-thio-D-glucoside / heptyl 1-thio-glucoside


Type: D-saccharide / Mass: 294.408 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM
#37: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C51H96O15

-
Non-polymers , 20 types, 3607 molecules

#21: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5
#22: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#23: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#24: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#25: Chemical
ChemComp-PHO / PHEOPHYTIN A / Pheophytin


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5 / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56
#27: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C45H86O10
#29: Chemical
ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9 / Plastoquinone


Mass: 749.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C53H80O2 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Mass: 258.120 Da / Num. of mol.: 82 / Source method: obtained synthetically
#31: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#33: Chemical
ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#34: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 71 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#35: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#38: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#39: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#40: Chemical ChemComp-RRX / (3R)-beta,beta-caroten-3-ol / beta-Cryptoxanthin / Β-Cryptoxanthin


Mass: 552.872 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C40H56O
#41: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#42: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H34FeN4O4
#43: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3290 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.48 %
Crystal growTemperature: 285 K / Method: microbatch / pH: 6
Details: 5% PEG 1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM MES BUFFER pH 6.0, MICRO-BATCH METHOD UNDER OIL, TMPERATURE 285K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→19.99 Å / Num. obs: 628112 / % possible obs: 99.6 % / Redundancy: 6.808 % / Biso Wilson estimate: 39.777 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.086 / Χ2: 1.036 / Net I/σ(I): 15.81 / Num. measured all: 4275973
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-2.016.8231.2121.631007400.7351.31199.4
2.01-2.156.6080.6613.01947300.8880.71899.5
2.15-2.327.0730.385.41885470.9630.4199.8
2.32-2.546.8080.2228.69816710.9840.24199.9
2.54-2.846.8730.12614.36738010.9940.13699.6
2.84-3.286.9020.07523.14654240.9970.08199.8
3.28-4.026.7830.04338.26553790.9990.04699.5
4.02-5.666.5560.03250.8431990.9990.03599.5

-
Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
PHENIX1.17.1_3660refinement
REFMAC5.8.0103refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WU2

3wu2


Resolution: 1.9→19.99 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1771 31327 5.01 %
Rwork0.1467 593996 -
obs0.1482 625323 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.25 Å2 / Biso mean: 43.9454 Å2 / Biso min: 15.46 Å2
Refinement stepCycle: final / Resolution: 1.9→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41221 0 10242 3409 54872
Biso mean--52.48 50.67 -
Num. residues----5298
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3156X-RAY DIFFRACTION10.261TORSIONAL
12a3156X-RAY DIFFRACTION10.261TORSIONAL
21B5620X-RAY DIFFRACTION10.261TORSIONAL
22b5620X-RAY DIFFRACTION10.261TORSIONAL
31C4998X-RAY DIFFRACTION10.261TORSIONAL
32c4998X-RAY DIFFRACTION10.261TORSIONAL
41D3484X-RAY DIFFRACTION10.261TORSIONAL
42d3484X-RAY DIFFRACTION10.261TORSIONAL
51E722X-RAY DIFFRACTION10.261TORSIONAL
52e722X-RAY DIFFRACTION10.261TORSIONAL
61F342X-RAY DIFFRACTION10.261TORSIONAL
62f342X-RAY DIFFRACTION10.261TORSIONAL
71H0X-RAY DIFFRACTION10.261TORSIONAL
72h0X-RAY DIFFRACTION10.261TORSIONAL
81I0X-RAY DIFFRACTION10.261TORSIONAL
82i0X-RAY DIFFRACTION10.261TORSIONAL
91J346X-RAY DIFFRACTION10.261TORSIONAL
92j346X-RAY DIFFRACTION10.261TORSIONAL
101K436X-RAY DIFFRACTION10.261TORSIONAL
102k436X-RAY DIFFRACTION10.261TORSIONAL
111L418X-RAY DIFFRACTION10.261TORSIONAL
112l418X-RAY DIFFRACTION10.261TORSIONAL
121M0X-RAY DIFFRACTION10.261TORSIONAL
122m0X-RAY DIFFRACTION10.261TORSIONAL
131O2237X-RAY DIFFRACTION10.261TORSIONAL
132o2237X-RAY DIFFRACTION10.261TORSIONAL
141T330X-RAY DIFFRACTION10.261TORSIONAL
142t330X-RAY DIFFRACTION10.261TORSIONAL
151U956X-RAY DIFFRACTION10.261TORSIONAL
152u956X-RAY DIFFRACTION10.261TORSIONAL
161V1340X-RAY DIFFRACTION10.261TORSIONAL
162v1340X-RAY DIFFRACTION10.261TORSIONAL
171X321X-RAY DIFFRACTION10.261TORSIONAL
172x321X-RAY DIFFRACTION10.261TORSIONAL
181Y258X-RAY DIFFRACTION10.261TORSIONAL
182y258X-RAY DIFFRACTION10.261TORSIONAL
191Z470X-RAY DIFFRACTION10.261TORSIONAL
192z470X-RAY DIFFRACTION10.261TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.920.328810060.30781970999
1.92-1.940.309510350.286519598100
1.94-1.970.283210560.266719608100
1.97-1.990.28310560.256619663100
1.99-2.020.268210850.239119608100
2.02-2.050.245910610.227419743100
2.05-2.080.246810330.215419682100
2.08-2.110.244210360.212219616100
2.11-2.140.24059840.20041956599
2.14-2.170.219510160.181719761100
2.17-2.210.220810020.174219786100
2.21-2.250.199910300.164119726100
2.25-2.30.199710300.160319802100
2.3-2.340.195710490.15119681100
2.34-2.390.185110280.145519830100
2.39-2.450.183310000.14219839100
2.45-2.510.172710480.134419838100
2.51-2.580.177210670.13851958199
2.58-2.650.166910540.128519776100
2.65-2.740.167610580.128419828100
2.74-2.840.172710250.127319800100
2.84-2.950.167610680.127219834100
2.95-3.080.174210090.131719913100
3.08-3.250.161911040.130519852100
3.25-3.450.159710620.12741968699
3.45-3.710.159810340.129420025100
3.71-4.080.157210720.124619958100
4.08-4.670.142710610.120320060100
4.67-5.860.159410410.13152011399
Refinement TLS params.Method: refined / Origin x: -13.3005 Å / Origin y: -13.5744 Å / Origin z: 25.7266 Å
111213212223313233
T0.1464 Å20.0341 Å2-0.0181 Å2-0.2252 Å2-0.0357 Å2--0.2057 Å2
L0.1266 °20.054 °2-0.0229 °2-0.3458 °2-0.152 °2--0.3867 °2
S-0.0068 Å °0.023 Å °-0.0207 Å °0.0303 Å °0.0417 Å °0.0054 Å °-0.0632 Å °-0.0045 Å °-0.0321 Å °
Refinement TLS groupSelection details: all

+
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.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
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.
  • 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

Read more