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- PDB-5t61: TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE FROM METHANO... -

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基本情報

登録情報
データベース: PDB / ID: 5t61
タイトルTUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE FROM METHANOTHERMOBACTER WOLFEII, TRICLINIC FORM AT 2.55 A
要素
  • (Tungsten formylmethanofuran dehydrogenase subunit ...) x 5
  • Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
キーワードOXIDOREDUCTASE / CO2 fixation / metallohydrolase / formate dehydrogenase / tungstopterin / methanogenesis / green house gas / methanothermobacter wolfeii / iron sulfur cluster / ferredoxin / beta helicoidal / channel / formate / CO2 / methanofuran / formylmethanofuran / nanomachine / binuclear center / tungsten / gate / coupling / enzyme / anaerobic / carboxylysine
機能・相同性HYDROSULFURIC ACID / : / Chem-MFN / Chem-MGD / IRON/SULFUR CLUSTER / :
機能・相同性情報
生物種Methanothermobacter wolfeii (古細菌)
Methanothermobacter sp. CaT2 (古細菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.55 Å
データ登録者Wagner, T. / Ermler, U. / Shima, S.
資金援助 ドイツ, 日本, 2件
組織認可番号国
Max Planck Society ドイツ
PRESTO 日本
引用ジャーナル: Science / 年: 2016
タイトル: The methanogenic CO2 reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters.
著者: Wagner, T. / Ermler, U. / Shima, S.
履歴
登録2016年9月1日登録サイト: RCSB / 処理サイト: PDBE
改定 1.02016年10月19日Provider: repository / タイプ: Initial release
改定 1.12016年12月21日Group: Database references
改定 1.22019年2月20日Group: Advisory / Data collection / Derived calculations
カテゴリ: pdbx_data_processing_status / pdbx_seq_map_depositor_info ...pdbx_data_processing_status / pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
改定 1.32024年1月17日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Tungsten formylmethanofuran dehydrogenase subunit fwdA
B: Tungsten formylmethanofuran dehydrogenase subunit B
C: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
D: Tungsten formylmethanofuran dehydrogenase subunit fwdD
E: Tungsten formylmethanofuran dehydrogenase subunit fwdG
F: Tungsten formylmethanofuran dehydrogenase subunit fwdF
G: Tungsten formylmethanofuran dehydrogenase subunit fwdA
H: Tungsten formylmethanofuran dehydrogenase subunit B
I: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
J: Tungsten formylmethanofuran dehydrogenase subunit fwdD
K: Tungsten formylmethanofuran dehydrogenase subunit fwdG
L: Tungsten formylmethanofuran dehydrogenase subunit fwdF
M: Tungsten formylmethanofuran dehydrogenase subunit fwdA
N: Tungsten formylmethanofuran dehydrogenase subunit B
O: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
P: Tungsten formylmethanofuran dehydrogenase subunit fwdD
Q: Tungsten formylmethanofuran dehydrogenase subunit fwdG
R: Tungsten formylmethanofuran dehydrogenase subunit fwdF
S: Tungsten formylmethanofuran dehydrogenase subunit fwdA
T: Tungsten formylmethanofuran dehydrogenase subunit B
U: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
V: Tungsten formylmethanofuran dehydrogenase subunit fwdD
W: Tungsten formylmethanofuran dehydrogenase subunit fwdG
X: Tungsten formylmethanofuran dehydrogenase subunit fwdF
Y: Tungsten formylmethanofuran dehydrogenase subunit fwdA
Z: Tungsten formylmethanofuran dehydrogenase subunit B
a: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
b: Tungsten formylmethanofuran dehydrogenase subunit fwdD
c: Tungsten formylmethanofuran dehydrogenase subunit fwdG
d: Tungsten formylmethanofuran dehydrogenase subunit fwdF
e: Tungsten formylmethanofuran dehydrogenase subunit fwdA
f: Tungsten formylmethanofuran dehydrogenase subunit B
g: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
h: Tungsten formylmethanofuran dehydrogenase subunit fwdD
i: Tungsten formylmethanofuran dehydrogenase subunit fwdG
j: Tungsten formylmethanofuran dehydrogenase subunit fwdF
k: Tungsten formylmethanofuran dehydrogenase subunit fwdA
l: Tungsten formylmethanofuran dehydrogenase subunit B
m: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
n: Tungsten formylmethanofuran dehydrogenase subunit fwdD
o: Tungsten formylmethanofuran dehydrogenase subunit fwdG
p: Tungsten formylmethanofuran dehydrogenase subunit fwdF
q: Tungsten formylmethanofuran dehydrogenase subunit fwdA
r: Tungsten formylmethanofuran dehydrogenase subunit B
s: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
t: Tungsten formylmethanofuran dehydrogenase subunit fwdD
u: Tungsten formylmethanofuran dehydrogenase subunit fwdG
v: Tungsten formylmethanofuran dehydrogenase subunit fwdF
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,667,213269
ポリマ－1,611,39048
非ポリマー55,823221
水11,043613
1
A: Tungsten formylmethanofuran dehydrogenase subunit fwdA
B: Tungsten formylmethanofuran dehydrogenase subunit B
C: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
D: Tungsten formylmethanofuran dehydrogenase subunit fwdD
E: Tungsten formylmethanofuran dehydrogenase subunit fwdG
F: Tungsten formylmethanofuran dehydrogenase subunit fwdF
G: Tungsten formylmethanofuran dehydrogenase subunit fwdA
H: Tungsten formylmethanofuran dehydrogenase subunit B
I: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
J: Tungsten formylmethanofuran dehydrogenase subunit fwdD
K: Tungsten formylmethanofuran dehydrogenase subunit fwdG
L: Tungsten formylmethanofuran dehydrogenase subunit fwdF
M: Tungsten formylmethanofuran dehydrogenase subunit fwdA
N: Tungsten formylmethanofuran dehydrogenase subunit B
O: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
P: Tungsten formylmethanofuran dehydrogenase subunit fwdD
Q: Tungsten formylmethanofuran dehydrogenase subunit fwdG
R: Tungsten formylmethanofuran dehydrogenase subunit fwdF
S: Tungsten formylmethanofuran dehydrogenase subunit fwdA
T: Tungsten formylmethanofuran dehydrogenase subunit B
U: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
V: Tungsten formylmethanofuran dehydrogenase subunit fwdD
W: Tungsten formylmethanofuran dehydrogenase subunit fwdG
X: Tungsten formylmethanofuran dehydrogenase subunit fwdF
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)833,499132
ポリマ－805,69524
非ポリマー27,804108
水43224
タイプ名称対称操作数
identity operation1_555x,y,z1
2
Y: Tungsten formylmethanofuran dehydrogenase subunit fwdA
Z: Tungsten formylmethanofuran dehydrogenase subunit B
a: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
b: Tungsten formylmethanofuran dehydrogenase subunit fwdD
c: Tungsten formylmethanofuran dehydrogenase subunit fwdG
d: Tungsten formylmethanofuran dehydrogenase subunit fwdF
e: Tungsten formylmethanofuran dehydrogenase subunit fwdA
f: Tungsten formylmethanofuran dehydrogenase subunit B
g: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
h: Tungsten formylmethanofuran dehydrogenase subunit fwdD
i: Tungsten formylmethanofuran dehydrogenase subunit fwdG
j: Tungsten formylmethanofuran dehydrogenase subunit fwdF
k: Tungsten formylmethanofuran dehydrogenase subunit fwdA
l: Tungsten formylmethanofuran dehydrogenase subunit B
m: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
n: Tungsten formylmethanofuran dehydrogenase subunit fwdD
o: Tungsten formylmethanofuran dehydrogenase subunit fwdG
p: Tungsten formylmethanofuran dehydrogenase subunit fwdF
q: Tungsten formylmethanofuran dehydrogenase subunit fwdA
r: Tungsten formylmethanofuran dehydrogenase subunit B
s: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
t: Tungsten formylmethanofuran dehydrogenase subunit fwdD
u: Tungsten formylmethanofuran dehydrogenase subunit fwdG
v: Tungsten formylmethanofuran dehydrogenase subunit fwdF
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)833,714137
ポリマ－805,69524
非ポリマー28,019113
水43224
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)174.183, 173.681, 183.162
Angle α, β, γ (deg.)89.980, 95.420, 92.140
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain I and (resseq 3:8 or resseq 10:28 or resseq...
21(chain C and (resseq 3:8 or resseq 10:28 or resseq...
31(chain O and (resseq 3:8 or resseq 10:28 or resseq...
41(chain U and (resseq 3:8 or resseq 10:28 or resseq...
51(chain a and (resseq 3:8 or resseq 10:28 or resseq...
61(chain g and (resseq 3:8 or resseq 10:28 or resseq...
71(chain m and (resseq 3:8 or resseq 10:28 or resseq...
81(chain s and (resseq 3:8 or resseq 10:28 or resseq...
12(chain B and ((resid 1 and (name N or name...
22(chain H and ((resid 1 and (name N or name...
32(chain N and ((resid 1 and (name N or name...
42(chain T and ((resid 1 and (name N or name...
52(chain Z and ((resid 1 and (name N or name...
62(chain f and ((resid 1 and (name N or name...
72(chain l and ((resid 1 and (name N or name...
82(chain r and ((resid 1 and (name N or name...
13(chain F and ((resid 7 and (name N or name...
23(chain L and ((resid 7 and (name N or name...
33(chain R and ((resid 7 and (name N or name...
43(chain X and ((resid 7 and (name N or name...
53(chain d and ((resid 7 and (name N or name...
63(chain j and ((resid 7 and (name N or name...
73(chain p and ((resid 7 and (name N or name...
83(chain v and ((resid 7 and (name N or name...
14(chain D and ((resid 1 and (name N or name...
24(chain J and ((resid 1 and (name N or name...
34(chain P and ((resid 1 and (name N or name...
44(chain V and ((resid 1 and (name N or name...
54(chain b and ((resid 1 and (name N or name...
64(chain h and ((resid 1 and (name N or name...
74(chain n and ((resid 1 and (name N or name...
84(chain t and ((resid 1 and (name N or name...
15(chain E and ((resid 2 and (name O or name...
25(chain K and ((resid 2 and (name N or name...
35(chain Q and ((resid 2 and (name N or name...
45(chain W and ((resid 2 and (name N or name...
55(chain c and ((resid 2 and (name N or name...
65(chain i and ((resid 2 and (name N or name...
75(chain o and ((resid 2 and (name N or name...
85(chain u and ((resid 2 and (name N or name...
16(chain A and (resseq 2:22 or (resid 23 and (name...
26(chain G and (resseq 2:22 or (resid 23 and (name...
36(chain M and (resseq 2:22 or (resid 23 and (name...
46(chain S and (resseq 2:22 or (resid 23 and (name...
56(chain Y and (resseq 2:22 or (resid 23 and (name...
66(chain e and (resseq 2:22 or (resid 23 and (name...
76(chain k and (resseq 2:22 or (resid 23 and (name...
86(chain q and (resseq 2:22 or (resid 23 and (name...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain I and (resseq 3:8 or resseq 10:28 or resseq...I3 - 8
121(chain I and (resseq 3:8 or resseq 10:28 or resseq...I10 - 28
131(chain I and (resseq 3:8 or resseq 10:28 or resseq...I30 - 31
141(chain I and (resseq 3:8 or resseq 10:28 or resseq...I33 - 43
151(chain I and (resseq 3:8 or resseq 10:28 or resseq...I45 - 50
161(chain I and (resseq 3:8 or resseq 10:28 or resseq...I51
171(chain I and (resseq 3:8 or resseq 10:28 or resseq...I2 - 270
181(chain I and (resseq 3:8 or resseq 10:28 or resseq...I2 - 270
191(chain I and (resseq 3:8 or resseq 10:28 or resseq...I2 - 270
1101(chain I and (resseq 3:8 or resseq 10:28 or resseq...I2 - 270
1111(chain I and (resseq 3:8 or resseq 10:28 or resseq...I2 - 270
1121(chain I and (resseq 3:8 or resseq 10:28 or resseq...I2 - 270
211(chain C and (resseq 3:8 or resseq 10:28 or resseq...C3 - 8
221(chain C and (resseq 3:8 or resseq 10:28 or resseq...C10 - 28
231(chain C and (resseq 3:8 or resseq 10:28 or resseq...C30 - 31
241(chain C and (resseq 3:8 or resseq 10:28 or resseq...C33 - 43
251(chain C and (resseq 3:8 or resseq 10:28 or resseq...C45 - 50
261(chain C and (resseq 3:8 or resseq 10:28 or resseq...C51
271(chain C and (resseq 3:8 or resseq 10:28 or resseq...C2 - 268
281(chain C and (resseq 3:8 or resseq 10:28 or resseq...C2 - 268
291(chain C and (resseq 3:8 or resseq 10:28 or resseq...C2 - 268
2101(chain C and (resseq 3:8 or resseq 10:28 or resseq...C2 - 268
2111(chain C and (resseq 3:8 or resseq 10:28 or resseq...C2 - 268
2121(chain C and (resseq 3:8 or resseq 10:28 or resseq...C2 - 268
311(chain O and (resseq 3:8 or resseq 10:28 or resseq...O3 - 8
321(chain O and (resseq 3:8 or resseq 10:28 or resseq...O10 - 28
331(chain O and (resseq 3:8 or resseq 10:28 or resseq...O30 - 31
341(chain O and (resseq 3:8 or resseq 10:28 or resseq...O33 - 43
351(chain O and (resseq 3:8 or resseq 10:28 or resseq...O45 - 50
361(chain O and (resseq 3:8 or resseq 10:28 or resseq...O51
371(chain O and (resseq 3:8 or resseq 10:28 or resseq...O2 - 269
381(chain O and (resseq 3:8 or resseq 10:28 or resseq...O2 - 269
391(chain O and (resseq 3:8 or resseq 10:28 or resseq...O2 - 269
3101(chain O and (resseq 3:8 or resseq 10:28 or resseq...O2 - 269
3111(chain O and (resseq 3:8 or resseq 10:28 or resseq...O2 - 269
3121(chain O and (resseq 3:8 or resseq 10:28 or resseq...O2 - 269
411(chain U and (resseq 3:8 or resseq 10:28 or resseq...U3 - 8
421(chain U and (resseq 3:8 or resseq 10:28 or resseq...U10 - 28
431(chain U and (resseq 3:8 or resseq 10:28 or resseq...U30 - 31
441(chain U and (resseq 3:8 or resseq 10:28 or resseq...U33 - 43
451(chain U and (resseq 3:8 or resseq 10:28 or resseq...U45 - 50
461(chain U and (resseq 3:8 or resseq 10:28 or resseq...U51
471(chain U and (resseq 3:8 or resseq 10:28 or resseq...U2 - 269
481(chain U and (resseq 3:8 or resseq 10:28 or resseq...U2 - 269
491(chain U and (resseq 3:8 or resseq 10:28 or resseq...U2 - 269
4101(chain U and (resseq 3:8 or resseq 10:28 or resseq...U2 - 269
4111(chain U and (resseq 3:8 or resseq 10:28 or resseq...U2 - 269
4121(chain U and (resseq 3:8 or resseq 10:28 or resseq...U2 - 269
511(chain a and (resseq 3:8 or resseq 10:28 or resseq...a3 - 8
521(chain a and (resseq 3:8 or resseq 10:28 or resseq...a10 - 28
531(chain a and (resseq 3:8 or resseq 10:28 or resseq...a30 - 31
541(chain a and (resseq 3:8 or resseq 10:28 or resseq...a33 - 43
551(chain a and (resseq 3:8 or resseq 10:28 or resseq...a45 - 50
561(chain a and (resseq 3:8 or resseq 10:28 or resseq...a51
571(chain a and (resseq 3:8 or resseq 10:28 or resseq...a2 - 269
581(chain a and (resseq 3:8 or resseq 10:28 or resseq...a2 - 269
591(chain a and (resseq 3:8 or resseq 10:28 or resseq...a2 - 269
5101(chain a and (resseq 3:8 or resseq 10:28 or resseq...a2 - 269
5111(chain a and (resseq 3:8 or resseq 10:28 or resseq...a2 - 269
5121(chain a and (resseq 3:8 or resseq 10:28 or resseq...a2 - 269
611(chain g and (resseq 3:8 or resseq 10:28 or resseq...g3 - 8
621(chain g and (resseq 3:8 or resseq 10:28 or resseq...g10 - 28
631(chain g and (resseq 3:8 or resseq 10:28 or resseq...g30 - 31
641(chain g and (resseq 3:8 or resseq 10:28 or resseq...g33 - 43
651(chain g and (resseq 3:8 or resseq 10:28 or resseq...g45 - 50
661(chain g and (resseq 3:8 or resseq 10:28 or resseq...g51
671(chain g and (resseq 3:8 or resseq 10:28 or resseq...g2 - 269
681(chain g and (resseq 3:8 or resseq 10:28 or resseq...g2 - 269
691(chain g and (resseq 3:8 or resseq 10:28 or resseq...g2 - 269
6101(chain g and (resseq 3:8 or resseq 10:28 or resseq...g2 - 269
6111(chain g and (resseq 3:8 or resseq 10:28 or resseq...g2 - 269
6121(chain g and (resseq 3:8 or resseq 10:28 or resseq...g2 - 269
711(chain m and (resseq 3:8 or resseq 10:28 or resseq...m3 - 8
721(chain m and (resseq 3:8 or resseq 10:28 or resseq...m10 - 28
731(chain m and (resseq 3:8 or resseq 10:28 or resseq...m30 - 31
741(chain m and (resseq 3:8 or resseq 10:28 or resseq...m33 - 43
751(chain m and (resseq 3:8 or resseq 10:28 or resseq...m45 - 50
761(chain m and (resseq 3:8 or resseq 10:28 or resseq...m51
771(chain m and (resseq 3:8 or resseq 10:28 or resseq...m2 - 269
781(chain m and (resseq 3:8 or resseq 10:28 or resseq...m2 - 269
791(chain m and (resseq 3:8 or resseq 10:28 or resseq...m2 - 269
7101(chain m and (resseq 3:8 or resseq 10:28 or resseq...m2 - 269
7111(chain m and (resseq 3:8 or resseq 10:28 or resseq...m2 - 269
7121(chain m and (resseq 3:8 or resseq 10:28 or resseq...m2 - 269
811(chain s and (resseq 3:8 or resseq 10:28 or resseq...s3 - 8
821(chain s and (resseq 3:8 or resseq 10:28 or resseq...s10 - 28
831(chain s and (resseq 3:8 or resseq 10:28 or resseq...s30 - 31
841(chain s and (resseq 3:8 or resseq 10:28 or resseq...s33 - 43
851(chain s and (resseq 3:8 or resseq 10:28 or resseq...s45 - 50
861(chain s and (resseq 3:8 or resseq 10:28 or resseq...s51
871(chain s and (resseq 3:8 or resseq 10:28 or resseq...s2 - 271
881(chain s and (resseq 3:8 or resseq 10:28 or resseq...s2 - 271
891(chain s and (resseq 3:8 or resseq 10:28 or resseq...s2 - 271
8101(chain s and (resseq 3:8 or resseq 10:28 or resseq...s2 - 271
8111(chain s and (resseq 3:8 or resseq 10:28 or resseq...s2 - 271
8121(chain s and (resseq 3:8 or resseq 10:28 or resseq...s2 - 271
112(chain B and ((resid 1 and (name N or name...B1
122(chain B and ((resid 1 and (name N or name...B1 - 455
132(chain B and ((resid 1 and (name N or name...B1 - 455
142(chain B and ((resid 1 and (name N or name...B1 - 455
152(chain B and ((resid 1 and (name N or name...B1 - 455
162(chain B and ((resid 1 and (name N or name...B1 - 455
212(chain H and ((resid 1 and (name N or name...H1
222(chain H and ((resid 1 and (name N or name...H1 - 429
232(chain H and ((resid 1 and (name N or name...H1 - 429
242(chain H and ((resid 1 and (name N or name...H1 - 429
252(chain H and ((resid 1 and (name N or name...H1 - 429
262(chain H and ((resid 1 and (name N or name...H1 - 429
312(chain N and ((resid 1 and (name N or name...N1
322(chain N and ((resid 1 and (name N or name...N1 - 430
332(chain N and ((resid 1 and (name N or name...N1 - 430
342(chain N and ((resid 1 and (name N or name...N1 - 430
352(chain N and ((resid 1 and (name N or name...N1 - 430
362(chain N and ((resid 1 and (name N or name...N1 - 430
412(chain T and ((resid 1 and (name N or name...T1
422(chain T and ((resid 1 and (name N or name...T1 - 429
432(chain T and ((resid 1 and (name N or name...T1 - 429
442(chain T and ((resid 1 and (name N or name...T1 - 429
452(chain T and ((resid 1 and (name N or name...T1 - 429
462(chain T and ((resid 1 and (name N or name...T1 - 429
512(chain Z and ((resid 1 and (name N or name...Z1
522(chain Z and ((resid 1 and (name N or name...Z1 - 430
532(chain Z and ((resid 1 and (name N or name...Z1 - 430
542(chain Z and ((resid 1 and (name N or name...Z1 - 430
552(chain Z and ((resid 1 and (name N or name...Z1 - 430
562(chain Z and ((resid 1 and (name N or name...Z1 - 430
612(chain f and ((resid 1 and (name N or name...f1
622(chain f and ((resid 1 and (name N or name...f1 - 429
632(chain f and ((resid 1 and (name N or name...f1 - 429
642(chain f and ((resid 1 and (name N or name...f1 - 429
652(chain f and ((resid 1 and (name N or name...f1 - 429
662(chain f and ((resid 1 and (name N or name...f1 - 429
712(chain l and ((resid 1 and (name N or name...l1
722(chain l and ((resid 1 and (name N or name...l1 - 430
732(chain l and ((resid 1 and (name N or name...l1 - 430
742(chain l and ((resid 1 and (name N or name...l1 - 430
752(chain l and ((resid 1 and (name N or name...l1 - 430
762(chain l and ((resid 1 and (name N or name...l1 - 430
812(chain r and ((resid 1 and (name N or name...r1
822(chain r and ((resid 1 and (name N or name...r1 - 430
832(chain r and ((resid 1 and (name N or name...r1 - 430
842(chain r and ((resid 1 and (name N or name...r1 - 430
852(chain r and ((resid 1 and (name N or name...r1 - 430
862(chain r and ((resid 1 and (name N or name...r1 - 430
113(chain F and ((resid 7 and (name N or name...F7
123(chain F and ((resid 7 and (name N or name...F3 - 349
133(chain F and ((resid 7 and (name N or name...F3 - 349
143(chain F and ((resid 7 and (name N or name...F3 - 349
153(chain F and ((resid 7 and (name N or name...F3 - 349
213(chain L and ((resid 7 and (name N or name...L7
223(chain L and ((resid 7 and (name N or name...L2 - 349
233(chain L and ((resid 7 and (name N or name...L2 - 349
243(chain L and ((resid 7 and (name N or name...L2 - 349
253(chain L and ((resid 7 and (name N or name...L2 - 349
313(chain R and ((resid 7 and (name N or name...R7
323(chain R and ((resid 7 and (name N or name...R6 - 349
333(chain R and ((resid 7 and (name N or name...R6 - 349
343(chain R and ((resid 7 and (name N or name...R6 - 349
353(chain R and ((resid 7 and (name N or name...R6 - 349
413(chain X and ((resid 7 and (name N or name...X7
423(chain X and ((resid 7 and (name N or name...X4 - 349
433(chain X and ((resid 7 and (name N or name...X4 - 349
443(chain X and ((resid 7 and (name N or name...X4 - 349
453(chain X and ((resid 7 and (name N or name...X4 - 349
513(chain d and ((resid 7 and (name N or name...d7
523(chain d and ((resid 7 and (name N or name...d7 - 349
533(chain d and ((resid 7 and (name N or name...d7 - 349
543(chain d and ((resid 7 and (name N or name...d7 - 349
553(chain d and ((resid 7 and (name N or name...d7 - 349
613(chain j and ((resid 7 and (name N or name...j7
623(chain j and ((resid 7 and (name N or name...j3 - 349
633(chain j and ((resid 7 and (name N or name...j3 - 349
643(chain j and ((resid 7 and (name N or name...j3 - 349
653(chain j and ((resid 7 and (name N or name...j3 - 349
713(chain p and ((resid 7 and (name N or name...p7
723(chain p and ((resid 7 and (name N or name...p2 - 349
733(chain p and ((resid 7 and (name N or name...p2 - 349
743(chain p and ((resid 7 and (name N or name...p2 - 349
753(chain p and ((resid 7 and (name N or name...p2 - 349
813(chain v and ((resid 7 and (name N or name...v7
823(chain v and ((resid 7 and (name N or name...v2 - 349
833(chain v and ((resid 7 and (name N or name...v2 - 349
843(chain v and ((resid 7 and (name N or name...v2 - 349
853(chain v and ((resid 7 and (name N or name...v2 - 349
114(chain D and ((resid 1 and (name N or name...D1
124(chain D and ((resid 1 and (name N or name...D1 - 129
134(chain D and ((resid 1 and (name N or name...D1 - 129
144(chain D and ((resid 1 and (name N or name...D1 - 129
154(chain D and ((resid 1 and (name N or name...D1 - 129
164(chain D and ((resid 1 and (name N or name...D1 - 129
214(chain J and ((resid 1 and (name N or name...J1
224(chain J and ((resid 1 and (name N or name...J1 - 129
234(chain J and ((resid 1 and (name N or name...J1 - 129
244(chain J and ((resid 1 and (name N or name...J1 - 129
254(chain J and ((resid 1 and (name N or name...J1 - 129
264(chain J and ((resid 1 and (name N or name...J1 - 129
314(chain P and ((resid 1 and (name N or name...P1
324(chain P and ((resid 1 and (name N or name...P1 - 129
334(chain P and ((resid 1 and (name N or name...P1 - 129
344(chain P and ((resid 1 and (name N or name...P1 - 129
354(chain P and ((resid 1 and (name N or name...P1 - 129
364(chain P and ((resid 1 and (name N or name...P1 - 129
414(chain V and ((resid 1 and (name N or name...V1
424(chain V and ((resid 1 and (name N or name...V1 - 129
434(chain V and ((resid 1 and (name N or name...V1 - 129
444(chain V and ((resid 1 and (name N or name...V1 - 129
454(chain V and ((resid 1 and (name N or name...V1 - 129
464(chain V and ((resid 1 and (name N or name...V1 - 129
514(chain b and ((resid 1 and (name N or name...b1
524(chain b and ((resid 1 and (name N or name...b1 - 129
534(chain b and ((resid 1 and (name N or name...b1 - 129
544(chain b and ((resid 1 and (name N or name...b1 - 129
554(chain b and ((resid 1 and (name N or name...b1 - 129
564(chain b and ((resid 1 and (name N or name...b1 - 129
614(chain h and ((resid 1 and (name N or name...h1
624(chain h and ((resid 1 and (name N or name...h1 - 129
634(chain h and ((resid 1 and (name N or name...h1 - 129
644(chain h and ((resid 1 and (name N or name...h1 - 129
654(chain h and ((resid 1 and (name N or name...h1 - 129
664(chain h and ((resid 1 and (name N or name...h1 - 129
714(chain n and ((resid 1 and (name N or name...n1
724(chain n and ((resid 1 and (name N or name...n1 - 129
734(chain n and ((resid 1 and (name N or name...n1 - 129
744(chain n and ((resid 1 and (name N or name...n1 - 129
754(chain n and ((resid 1 and (name N or name...n1 - 129
764(chain n and ((resid 1 and (name N or name...n1 - 129
814(chain t and ((resid 1 and (name N or name...t1
824(chain t and ((resid 1 and (name N or name...t1 - 129
834(chain t and ((resid 1 and (name N or name...t1 - 129
844(chain t and ((resid 1 and (name N or name...t1 - 129
854(chain t and ((resid 1 and (name N or name...t1 - 129
864(chain t and ((resid 1 and (name N or name...t1 - 129
115(chain E and ((resid 2 and (name O or name...E2
125(chain E and ((resid 2 and (name O or name...E2 - 81
135(chain E and ((resid 2 and (name O or name...E2 - 81
215(chain K and ((resid 2 and (name N or name...K2
225(chain K and ((resid 2 and (name N or name...K2 - 81
235(chain K and ((resid 2 and (name N or name...K2 - 81
315(chain Q and ((resid 2 and (name N or name...Q2
325(chain Q and ((resid 2 and (name N or name...Q2 - 81
335(chain Q and ((resid 2 and (name N or name...Q2 - 81
415(chain W and ((resid 2 and (name N or name...W2
425(chain W and ((resid 2 and (name N or name...W2 - 81
435(chain W and ((resid 2 and (name N or name...W2 - 81
515(chain c and ((resid 2 and (name N or name...c2
525(chain c and ((resid 2 and (name N or name...c2 - 81
535(chain c and ((resid 2 and (name N or name...c2 - 81
615(chain i and ((resid 2 and (name N or name...i2
625(chain i and ((resid 2 and (name N or name...i2 - 81
635(chain i and ((resid 2 and (name N or name...i2 - 81
715(chain o and ((resid 2 and (name N or name...o2
725(chain o and ((resid 2 and (name N or name...o2 - 81
735(chain o and ((resid 2 and (name N or name...o2 - 81
815(chain u and ((resid 2 and (name N or name...u2
825(chain u and ((resid 2 and (name N or name...u2 - 82
835(chain u and ((resid 2 and (name N or name...u2 - 82
116(chain A and (resseq 2:22 or (resid 23 and (name...A2 - 22
126(chain A and (resseq 2:22 or (resid 23 and (name...A23
136(chain A and (resseq 2:22 or (resid 23 and (name...A1 - 569
146(chain A and (resseq 2:22 or (resid 23 and (name...A1 - 569
156(chain A and (resseq 2:22 or (resid 23 and (name...A1 - 569
166(chain A and (resseq 2:22 or (resid 23 and (name...A1 - 569
176(chain A and (resseq 2:22 or (resid 23 and (name...A1 - 569
186(chain A and (resseq 2:22 or (resid 23 and (name...A1 - 569
216(chain G and (resseq 2:22 or (resid 23 and (name...G2 - 22
226(chain G and (resseq 2:22 or (resid 23 and (name...G23
236(chain G and (resseq 2:22 or (resid 23 and (name...G2 - 569
246(chain G and (resseq 2:22 or (resid 23 and (name...G2 - 569
256(chain G and (resseq 2:22 or (resid 23 and (name...G2 - 569
266(chain G and (resseq 2:22 or (resid 23 and (name...G2 - 569
276(chain G and (resseq 2:22 or (resid 23 and (name...G2 - 569
286(chain G and (resseq 2:22 or (resid 23 and (name...G2 - 569
316(chain M and (resseq 2:22 or (resid 23 and (name...M2 - 22
326(chain M and (resseq 2:22 or (resid 23 and (name...M23
336(chain M and (resseq 2:22 or (resid 23 and (name...M2 - 569
346(chain M and (resseq 2:22 or (resid 23 and (name...M2 - 569
356(chain M and (resseq 2:22 or (resid 23 and (name...M2 - 569
366(chain M and (resseq 2:22 or (resid 23 and (name...M2 - 569
376(chain M and (resseq 2:22 or (resid 23 and (name...M2 - 569
386(chain M and (resseq 2:22 or (resid 23 and (name...M2 - 569
416(chain S and (resseq 2:22 or (resid 23 and (name...S2 - 22
426(chain S and (resseq 2:22 or (resid 23 and (name...S23
436(chain S and (resseq 2:22 or (resid 23 and (name...S1 - 569
446(chain S and (resseq 2:22 or (resid 23 and (name...S1 - 569
456(chain S and (resseq 2:22 or (resid 23 and (name...S1 - 569
466(chain S and (resseq 2:22 or (resid 23 and (name...S1 - 569
476(chain S and (resseq 2:22 or (resid 23 and (name...S1 - 569
486(chain S and (resseq 2:22 or (resid 23 and (name...S1 - 569
516(chain Y and (resseq 2:22 or (resid 23 and (name...Y2 - 22
526(chain Y and (resseq 2:22 or (resid 23 and (name...Y23
536(chain Y and (resseq 2:22 or (resid 23 and (name...Y2 - 569
546(chain Y and (resseq 2:22 or (resid 23 and (name...Y2 - 569
556(chain Y and (resseq 2:22 or (resid 23 and (name...Y2 - 569
566(chain Y and (resseq 2:22 or (resid 23 and (name...Y2 - 569
576(chain Y and (resseq 2:22 or (resid 23 and (name...Y2 - 569
586(chain Y and (resseq 2:22 or (resid 23 and (name...Y2 - 569
616(chain e and (resseq 2:22 or (resid 23 and (name...e2 - 22
626(chain e and (resseq 2:22 or (resid 23 and (name...e23
636(chain e and (resseq 2:22 or (resid 23 and (name...e1 - 569
646(chain e and (resseq 2:22 or (resid 23 and (name...e1 - 569
656(chain e and (resseq 2:22 or (resid 23 and (name...e1 - 569
666(chain e and (resseq 2:22 or (resid 23 and (name...e1 - 569
676(chain e and (resseq 2:22 or (resid 23 and (name...e1 - 569
686(chain e and (resseq 2:22 or (resid 23 and (name...e1 - 569
716(chain k and (resseq 2:22 or (resid 23 and (name...k2 - 22
726(chain k and (resseq 2:22 or (resid 23 and (name...k23
736(chain k and (resseq 2:22 or (resid 23 and (name...k2 - 569
746(chain k and (resseq 2:22 or (resid 23 and (name...k2 - 569
756(chain k and (resseq 2:22 or (resid 23 and (name...k2 - 569
766(chain k and (resseq 2:22 or (resid 23 and (name...k2 - 569
776(chain k and (resseq 2:22 or (resid 23 and (name...k2 - 569
786(chain k and (resseq 2:22 or (resid 23 and (name...k2 - 569
816(chain q and (resseq 2:22 or (resid 23 and (name...q2 - 22
826(chain q and (resseq 2:22 or (resid 23 and (name...q23
836(chain q and (resseq 2:22 or (resid 23 and (name...q1 - 569
846(chain q and (resseq 2:22 or (resid 23 and (name...q1 - 569
856(chain q and (resseq 2:22 or (resid 23 and (name...q1 - 569
866(chain q and (resseq 2:22 or (resid 23 and (name...q1 - 569
876(chain q and (resseq 2:22 or (resid 23 and (name...q1 - 569
886(chain q and (resseq 2:22 or (resid 23 and (name...q1 - 569

NCSアンサンブル:
ID
1
2
3
4
5
6

-
要素

-
Tungsten formylmethanofuran dehydrogenase subunit ... , 5種, 40分子 AGMSYekqBHNTZflrDJPVbhntEKQWci...

#1: タンパク質
Tungsten formylmethanofuran dehydrogenase subunit fwdA


分子量: 62806.594 Da / 分子数: 8 / 由来タイプ: 天然
詳細: FwdA subunit contains a carboxylysine at position 178
由来: (天然) Methanothermobacter wolfeii (古細菌)
#2: タンパク質
Tungsten formylmethanofuran dehydrogenase subunit B


分子量: 48411.355 Da / 分子数: 8 / 由来タイプ: 天然 / 由来: (天然) Methanothermobacter sp. CaT2 (古細菌)
#4: タンパク質
Tungsten formylmethanofuran dehydrogenase subunit fwdD


分子量: 14408.779 Da / 分子数: 8 / 由来タイプ: 天然 / 由来: (天然) Methanothermobacter wolfeii (古細菌)
#5: タンパク質
Tungsten formylmethanofuran dehydrogenase subunit fwdG


分子量: 8564.948 Da / 分子数: 8 / 由来タイプ: 天然 / 由来: (天然) Methanothermobacter wolfeii (古細菌)
#6: タンパク質
Tungsten formylmethanofuran dehydrogenase subunit fwdF


分子量: 38618.570 Da / 分子数: 8 / 由来タイプ: 天然 / 由来: (天然) Methanothermobacter wolfeii (古細菌)

-
タンパク質 , 1種, 8分子 CIOUagms

#3: タンパク質
Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C / Tungsten-containing formylmethanofuran dehydrogenase II subunit C


分子量: 28613.471 Da / 分子数: 8 / 由来タイプ: 天然 / 由来: (天然) Methanothermobacter wolfeii (古細菌) / 参照: formylmethanofuran dehydrogenase

-
非ポリマー , 11種, 834分子

#7: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 16 / 由来タイプ: 合成 / 式: Zn
#8: 化合物
ChemComp-MFN / N-[4,5,7-TRICARBOXYHEPTANOYL]-L-GAMMA-GLUTAMYL-N-{2-[4-({5-[(FORMYLAMINO)METHYL]-3-FURYL}METHOXY)PHENYL]ETHYL}-D-GLUTAMINE


分子量: 776.741 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C35H44N4O16
#9: 化合物
ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 7 / 由来タイプ: 合成 / 式: Na
#10: 化合物...
ChemComp-K / POTASSIUM ION / カリウムカチオン


分子量: 39.098 Da / 分子数: 57 / 由来タイプ: 合成 / 式: K
#11: 化合物...
ChemComp-SF4 / IRON/SULFUR CLUSTER


分子量: 351.640 Da / 分子数: 92 / 由来タイプ: 合成 / 式: Fe4S4
#12: 化合物
ChemComp-W / TUNGSTEN ION


分子量: 183.840 Da / 分子数: 8 / 由来タイプ: 合成 / 式: W
#13: 化合物
ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


分子量: 740.557 Da / 分子数: 16 / 由来タイプ: 合成 / 式: C20H26N10O13P2S2
#14: 化合物
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / 硫化水素


分子量: 34.081 Da / 分子数: 8 / 由来タイプ: 合成 / 式: H2S
#15: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Mg
#16: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Cl
#17: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 613 / 由来タイプ: 天然 / 式: H2O

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.43 Å3/Da / 溶媒含有率: 64.17 %
解説: Brown plate crystals, the thickest plate give the best diffraction. Crystal can have a length of 600 um.
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8
詳細: 100 mM Tricine/NaOH, pH 8.0, 30% (v/v) pentaerythritol propoxylate 426 (5/4 PO/OH), and 400 mM KCl. The crystallized sample has to be anoxic and extremely fresh (crystallized after 3 days of ...詳細: 100 mM Tricine/NaOH, pH 8.0, 30% (v/v) pentaerythritol propoxylate 426 (5/4 PO/OH), and 400 mM KCl. The crystallized sample has to be anoxic and extremely fresh (crystallized after 3 days of purification) without any freezing step. The optimal protein concentration is about 20-35 mg/ml. Drops are made by mixing 1 ul protein and 1 ul precipitant. Crystals appeared after 3-5 days.
PH範囲: 7.5-8.5 / Temp details: Only one temperature has been tested

-
データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: SLS / ビームライン: X10SA / 波長: 1.00006 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2015年7月4日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.00006 Å / 相対比: 1
反射解像度: 2.55→49.08 Å / Num. obs: 673754 / % possible obs: 96.8 % / 冗長度: 2.6 % / CC1/2: 0.979 / Rmerge(I) obs: 0.14 / Rsym value: 0.1 / Net I/σ(I): 5.5
反射 シェル解像度: 2.55→2.69 Å / 冗長度: 2.4 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.465 / % possible all: 97

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
PDB_EXTRACT3.2データ抽出
XDSデータ削減
SCALA3.3.22データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ID : 5T5I

5t5i


解像度: 2.55→48.967 Å / SU ML: 0.38 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 26.88
Rfactor反射数%反射Selection details
Rfree0.2593 34085 5.06 %Random selection
Rwork0.2292 ---
obs0.2307 673055 96.68 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 151.68 Å2 / Biso mean: 46.5475 Å2 / Biso min: 15.84 Å2
精密化ステップサイクル: final / 解像度: 2.55→48.967 Å
タンパク質核酸リガンド溶媒全体
原子数111691 0 2017 613 114321
Biso mean--46.36 39.44 -
残基数----14548
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.008116322
X-RAY DIFFRACTIONf_angle_d1.594158599
X-RAY DIFFRACTIONf_chiral_restr0.16317744
X-RAY DIFFRACTIONf_plane_restr0.00620382
X-RAY DIFFRACTIONf_dihedral_angle_d17.81870055
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11I9086X-RAY DIFFRACTION9.502TORSIONAL
12C9086X-RAY DIFFRACTION9.502TORSIONAL
13O9086X-RAY DIFFRACTION9.502TORSIONAL
14U9086X-RAY DIFFRACTION9.502TORSIONAL
15a9086X-RAY DIFFRACTION9.502TORSIONAL
16g9086X-RAY DIFFRACTION9.502TORSIONAL
17m9086X-RAY DIFFRACTION9.502TORSIONAL
18s9086X-RAY DIFFRACTION9.502TORSIONAL
21B15684X-RAY DIFFRACTION9.502TORSIONAL
22H15684X-RAY DIFFRACTION9.502TORSIONAL
23N15684X-RAY DIFFRACTION9.502TORSIONAL
24T15684X-RAY DIFFRACTION9.502TORSIONAL
25Z15684X-RAY DIFFRACTION9.502TORSIONAL
26f15684X-RAY DIFFRACTION9.502TORSIONAL
27l15684X-RAY DIFFRACTION9.502TORSIONAL
28r15684X-RAY DIFFRACTION9.502TORSIONAL
31F11622X-RAY DIFFRACTION9.502TORSIONAL
32L11622X-RAY DIFFRACTION9.502TORSIONAL
33R11622X-RAY DIFFRACTION9.502TORSIONAL
34X11622X-RAY DIFFRACTION9.502TORSIONAL
35d11622X-RAY DIFFRACTION9.502TORSIONAL
36j11622X-RAY DIFFRACTION9.502TORSIONAL
37p11622X-RAY DIFFRACTION9.502TORSIONAL
38v11622X-RAY DIFFRACTION9.502TORSIONAL
41D4692X-RAY DIFFRACTION9.502TORSIONAL
42J4692X-RAY DIFFRACTION9.502TORSIONAL
43P4692X-RAY DIFFRACTION9.502TORSIONAL
44V4692X-RAY DIFFRACTION9.502TORSIONAL
45b4692X-RAY DIFFRACTION9.502TORSIONAL
46h4692X-RAY DIFFRACTION9.502TORSIONAL
47n4692X-RAY DIFFRACTION9.502TORSIONAL
48t4692X-RAY DIFFRACTION9.502TORSIONAL
51E2863X-RAY DIFFRACTION9.502TORSIONAL
52K2863X-RAY DIFFRACTION9.502TORSIONAL
53Q2863X-RAY DIFFRACTION9.502TORSIONAL
54W2863X-RAY DIFFRACTION9.502TORSIONAL
55c2863X-RAY DIFFRACTION9.502TORSIONAL
56i2863X-RAY DIFFRACTION9.502TORSIONAL
57o2863X-RAY DIFFRACTION9.502TORSIONAL
58u2863X-RAY DIFFRACTION9.502TORSIONAL
61A19793X-RAY DIFFRACTION9.502TORSIONAL
62G19793X-RAY DIFFRACTION9.502TORSIONAL
63M19793X-RAY DIFFRACTION9.502TORSIONAL
64S19793X-RAY DIFFRACTION9.502TORSIONAL
65Y19793X-RAY DIFFRACTION9.502TORSIONAL
66e19793X-RAY DIFFRACTION9.502TORSIONAL
67k19793X-RAY DIFFRACTION9.502TORSIONAL
68q19793X-RAY DIFFRACTION9.502TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.5790.367110440.3363206122165694
2.579-2.60930.365110450.3301214262247197
2.6093-2.64110.346410970.3187214882258597
2.6411-2.67460.340910810.309214952257698
2.6746-2.70980.325211690.288215132268298
2.7098-2.74690.318111460.2918214002254697
2.7469-2.78610.314211930.2848214312262498
2.7861-2.82770.327711500.2815214622261297
2.8277-2.87190.325311850.2821215902277598
2.8719-2.9190.327112560.2829213442260098
2.919-2.96930.302312040.2759215502275498
2.9693-3.02330.30311970.2673213222251997
3.0233-3.08140.30411760.2576214512262797
3.0814-3.14430.287711620.2575212762243897
3.1443-3.21260.292412080.2519214472265597
3.2126-3.28740.279912130.2458213132252697
3.2874-3.36960.264112700.2363211972246797
3.3696-3.46060.265112410.2288212562249797
3.4606-3.56240.260112290.2229212242245397
3.5624-3.67740.258911120.2237212932240597
3.6774-3.80880.250412200.2184211812240196
3.8088-3.96120.234811170.2126211572227496
3.9612-4.14140.233710580.2027211962225496
4.1414-4.35960.22488920.1999214032229596
4.3596-4.63260.208310730.1916209752204895
4.6326-4.98990.214411410.1966210522219395
4.9899-5.49150.21969290.2014212512218096
5.4915-6.28470.224910420.201212602230296
6.2847-7.91270.228911430.2022212092235296
7.9127-48.97630.225810920.2027211962228896

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る