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- PDB-4v67: Crystal structure of a translation termination complex formed wit... -

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基本情報

登録情報
データベース: PDB / ID: 4v67
タイトルCrystal structure of a translation termination complex formed with release factor RF2.
要素
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S RRNA
  • 23S RRNA23SリボソームRNA
  • 5S RRNA5SリボソームRNA
  • Bacterial peptide chain release factor 2 (RF-2)
  • MRNA伝令RNA
  • P AND E-SITE TRNA(FMET)
キーワードRIBOSOME (リボソーム) / RF2 / TERMINATION / TRNA (転移RNA)
機能・相同性
機能・相同性情報


translation release factor activity, codon specific / large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / リボソーム / structural constituent of ribosome ...translation release factor activity, codon specific / large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / リボソーム / structural constituent of ribosome / 翻訳 (生物学) / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / 細胞質
類似検索 - 分子機能
Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain / 30S ribosomal protein Thx / 30S ribosomal protein Thx ...Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, type Z / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein S14/S29 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L14P, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20
類似検索 - ドメイン・相同性
: / リボ核酸 / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bTHX ...: / リボ核酸 / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bTHX / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein bL28 / Peptide chain release factor 2 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35
類似検索 - 構成要素
生物種Thermus thermophilus (サーマス・サーモフィルス)
Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 解像度: 3 Å
データ登録者Korostelev, A. / Asahara, H. / Lancaster, L. / Laurberg, M. / Hirschi, A. / Noller, H.F.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2008
タイトル: Crystal structure of a translation termination complex formed with release factor RF2.
著者: Korostelev, A. / Asahara, H. / Lancaster, L. / Laurberg, M. / Hirschi, A. / Zhu, J. / Trakhanov, S. / Scott, W.G. / Noller, H.F.
履歴
登録2008年10月27日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年7月9日Provider: repository / タイプ: Initial release
置き換え2014年12月10日ID: 3F1E, 3F1F, 3F1G, 3F1H
改定 1.12014年12月10日Group: Other
改定 1.22023年9月20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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _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_PDB_ins_code / _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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _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_ref_seq_dif.details

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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
AA: 16S RRNA
AZ: P AND E-SITE TRNA(FMET)
AV: MRNA
AY: P AND E-SITE TRNA(FMET)
AB: 30S ribosomal protein S2
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AU: 30S ribosomal protein Thx
AX: Bacterial peptide chain release factor 2 (RF-2)
BA: 23S RRNA
BB: 5S RRNA
BD: 50S ribosomal protein L2
BE: 50S ribosomal protein L3
BF: 50S ribosomal protein L4
BG: 50S ribosomal protein L5
BH: 50S ribosomal protein L6
BI: 50S ribosomal protein L9
BK: 50S ribosomal protein L11
BN: 50S ribosomal protein L13
BO: 50S ribosomal protein L14
BP: 50S ribosomal protein L15
BQ: 50S ribosomal protein L16
BR: 50S ribosomal protein L17
BS: 50S ribosomal protein L18
BT: 50S ribosomal protein L19
BU: 50S ribosomal protein L20
BV: 50S ribosomal protein L21
BW: 50S ribosomal protein L22
BX: 50S ribosomal protein L23
BY: 50S ribosomal protein L24
BZ: 50S ribosomal protein L25
B0: 50S ribosomal protein L27
B1: 50S ribosomal protein L28
B2: 50S ribosomal protein L29
B3: 50S ribosomal protein L30
B4: 50S ribosomal protein L31
B5: 50S ribosomal protein L32
B6: 50S ribosomal protein L33
B7: 50S ribosomal protein L34
B8: 50S ribosomal protein L35
CA: 16S RRNA
CZ: P AND E-SITE TRNA(FMET)
CV: MRNA
CY: P AND E-SITE TRNA(FMET)
CB: 30S ribosomal protein S2
CC: 30S ribosomal protein S3
CD: 30S ribosomal protein S4
CE: 30S ribosomal protein S5
CF: 30S ribosomal protein S6
CG: 30S ribosomal protein S7
CH: 30S ribosomal protein S8
CI: 30S ribosomal protein S9
CJ: 30S ribosomal protein S10
CK: 30S ribosomal protein S11
CL: 30S ribosomal protein S12
CM: 30S ribosomal protein S13
CN: 30S ribosomal protein S14
CO: 30S ribosomal protein S15
CP: 30S ribosomal protein S16
CQ: 30S ribosomal protein S17
CR: 30S ribosomal protein S18
CS: 30S ribosomal protein S19
CT: 30S ribosomal protein S20
CU: 30S ribosomal protein Thx
CX: Bacterial peptide chain release factor 2 (RF-2)
DA: 23S RRNA
DB: 5S RRNA
DD: 50S ribosomal protein L2
DE: 50S ribosomal protein L3
DF: 50S ribosomal protein L4
DG: 50S ribosomal protein L5
DH: 50S ribosomal protein L6
DI: 50S ribosomal protein L9
DK: 50S ribosomal protein L11
DN: 50S ribosomal protein L13
DO: 50S ribosomal protein L14
DP: 50S ribosomal protein L15
DQ: 50S ribosomal protein L16
DR: 50S ribosomal protein L17
DS: 50S ribosomal protein L18
DT: 50S ribosomal protein L19
DU: 50S ribosomal protein L20
DV: 50S ribosomal protein L21
DW: 50S ribosomal protein L22
DX: 50S ribosomal protein L23
DY: 50S ribosomal protein L24
DZ: 50S ribosomal protein L25
D0: 50S ribosomal protein L27
D1: 50S ribosomal protein L28
D2: 50S ribosomal protein L29
D3: 50S ribosomal protein L30
D5: 50S ribosomal protein L32
D6: 50S ribosomal protein L33
D7: 50S ribosomal protein L34
D8: 50S ribosomal protein L35
D4: 50S ribosomal protein L31
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)4,621,7852504
ポリマ－4,563,483112
非ポリマー58,3022392
水0
1
AA: 16S RRNA
AZ: P AND E-SITE TRNA(FMET)
AV: MRNA
AY: P AND E-SITE TRNA(FMET)
AB: 30S ribosomal protein S2
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AU: 30S ribosomal protein Thx
AX: Bacterial peptide chain release factor 2 (RF-2)
BA: 23S RRNA
BB: 5S RRNA
BD: 50S ribosomal protein L2
BE: 50S ribosomal protein L3
BF: 50S ribosomal protein L4
BG: 50S ribosomal protein L5
BH: 50S ribosomal protein L6
BI: 50S ribosomal protein L9
BK: 50S ribosomal protein L11
BN: 50S ribosomal protein L13
BO: 50S ribosomal protein L14
BP: 50S ribosomal protein L15
BQ: 50S ribosomal protein L16
BR: 50S ribosomal protein L17
BS: 50S ribosomal protein L18
BT: 50S ribosomal protein L19
BU: 50S ribosomal protein L20
BV: 50S ribosomal protein L21
BW: 50S ribosomal protein L22
BX: 50S ribosomal protein L23
BY: 50S ribosomal protein L24
BZ: 50S ribosomal protein L25
B0: 50S ribosomal protein L27
B1: 50S ribosomal protein L28
B2: 50S ribosomal protein L29
B3: 50S ribosomal protein L30
B4: 50S ribosomal protein L31
B5: 50S ribosomal protein L32
B6: 50S ribosomal protein L33
B7: 50S ribosomal protein L34
B8: 50S ribosomal protein L35
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,320,4451645
ポリマ－2,281,74256
非ポリマー38,7031589
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
CA: 16S RRNA
CZ: P AND E-SITE TRNA(FMET)
CV: MRNA
CY: P AND E-SITE TRNA(FMET)
CB: 30S ribosomal protein S2
CC: 30S ribosomal protein S3
CD: 30S ribosomal protein S4
CE: 30S ribosomal protein S5
CF: 30S ribosomal protein S6
CG: 30S ribosomal protein S7
CH: 30S ribosomal protein S8
CI: 30S ribosomal protein S9
CJ: 30S ribosomal protein S10
CK: 30S ribosomal protein S11
CL: 30S ribosomal protein S12
CM: 30S ribosomal protein S13
CN: 30S ribosomal protein S14
CO: 30S ribosomal protein S15
CP: 30S ribosomal protein S16
CQ: 30S ribosomal protein S17
CR: 30S ribosomal protein S18
CS: 30S ribosomal protein S19
CT: 30S ribosomal protein S20
CU: 30S ribosomal protein Thx
CX: Bacterial peptide chain release factor 2 (RF-2)
DA: 23S RRNA
DB: 5S RRNA
DD: 50S ribosomal protein L2
DE: 50S ribosomal protein L3
DF: 50S ribosomal protein L4
DG: 50S ribosomal protein L5
DH: 50S ribosomal protein L6
DI: 50S ribosomal protein L9
DK: 50S ribosomal protein L11
DN: 50S ribosomal protein L13
DO: 50S ribosomal protein L14
DP: 50S ribosomal protein L15
DQ: 50S ribosomal protein L16
DR: 50S ribosomal protein L17
DS: 50S ribosomal protein L18
DT: 50S ribosomal protein L19
DU: 50S ribosomal protein L20
DV: 50S ribosomal protein L21
DW: 50S ribosomal protein L22
DX: 50S ribosomal protein L23
DY: 50S ribosomal protein L24
DZ: 50S ribosomal protein L25
D0: 50S ribosomal protein L27
D1: 50S ribosomal protein L28
D2: 50S ribosomal protein L29
D3: 50S ribosomal protein L30
D5: 50S ribosomal protein L32
D6: 50S ribosomal protein L33
D7: 50S ribosomal protein L34
D8: 50S ribosomal protein L35
D4: 50S ribosomal protein L31
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,301,341859
ポリマ－2,281,74256
非ポリマー19,599803
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)211.240, 456.780, 618.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27
18
28

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111(chain BA or chain BB or chain BD or chain...
211(chain DA or chain DB or chain DD or chain...
112chain AA or segid AS* or segid AT*
212chain CA or segid BS* or segid BT*
113chain AY or chain AV
213chain CY or chain CV
114chain AZ
214chain CZ
115chain AX and not resid 1:124
215chain CX and not resid 1:124
116chain AX and resid 1:124
216chain CX and resid 1:124
117chain BA and resid 2093:2196
217chain DA and resid 2093:2196
118chain BA and resid 1051:1108
218chain DA and resid 1051:1108

NCSアンサンブル:
ID
1
2
3
4
5
6
7
8

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要素

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RNA鎖 , 5種, 12分子 AACAAZAYCZCYAVCVBADABBDB

#1: RNA鎖 16S RRNA /


分子量: 494985.938 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: GenBank: 155076
#2: RNA鎖
P AND E-SITE TRNA(FMET)


分子量: 24802.785 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌)
#3: RNA鎖 MRNA / 伝令RNA


分子量: 8862.456 Da / 分子数: 2 / 由来タイプ: 合成
#25: RNA鎖 23S RRNA / 23SリボソームRNA


分子量: 941050.938 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27
#26: RNA鎖 5S RRNA / 5SリボソームRNA


分子量: 40152.945 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27

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30S ribosomal protein ... , 20種, 40分子 ABCBACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCP...

#4: タンパク質 30S ribosomal protein S2 /


分子量: 29317.703 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62662
#5: タンパク質 30S ribosomal protein S3 /


分子量: 26751.076 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62663
#6: タンパク質 30S ribosomal protein S4 /


分子量: 24373.447 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62664
#7: タンパク質 30S ribosomal protein S5 /


分子量: 17583.416 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62665
#8: タンパク質 30S ribosomal protein S6 /


分子量: 11988.753 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62666
#9: タンパク質 30S ribosomal protein S7 /


分子量: 18050.973 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62667
#10: タンパク質 30S ribosomal protein S8 /


分子量: 15868.570 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62668
#11: タンパク質 30S ribosomal protein S9 /


分子量: 14429.661 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62669
#12: タンパク質 30S ribosomal protein S10 /


分子量: 11954.968 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62653
#13: タンパク質 30S ribosomal protein S11 /


分子量: 13737.868 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62654
#14: タンパク質 30S ribosomal protein S12 /


分子量: 14821.621 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P61941
#15: タンパク質 30S ribosomal protein S13 /


分子量: 14338.861 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62655
#16: タンパク質 30S ribosomal protein S14 /


分子量: 7158.725 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62656
#17: タンパク質 30S ribosomal protein S15 /


分子量: 10578.407 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62657
#18: タンパク質 30S ribosomal protein S16 /


分子量: 10409.983 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62238
#19: タンパク質 30S ribosomal protein S17 /


分子量: 12324.670 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62658
#20: タンパク質 30S ribosomal protein S18 /


分子量: 10258.299 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62659
#21: タンパク質 30S ribosomal protein S19 /


分子量: 10605.464 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62660
#22: タンパク質 30S ribosomal protein S20 /


分子量: 11722.116 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62661
#23: タンパク質・ペプチド 30S ribosomal protein Thx / リボソーム


分子量: 3350.030 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62613

-
タンパク質 , 1種, 2分子 AXCX

#24: タンパク質 Bacterial peptide chain release factor 2 (RF-2) / RF2


分子量: 42793.469 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72GJ6

+
50S ribosomal protein ... , 29種, 58分子 BDDDBEDEBFDFBGDGBHDHBIDIBKDKBNDNBODOBPDPBQDQBRDRBSDSBTDTBUDU...

#27: タンパク質 50S ribosomal protein L2 /


分子量: 30532.551 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72I07
#28: タンパク質 50S ribosomal protein L3 /


分子量: 22450.213 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72I04
#29: タンパク質 50S ribosomal protein L4 /


分子量: 23303.980 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72I05
#30: タンパク質 50S ribosomal protein L5 /


分子量: 21075.623 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72I16
#31: タンパク質 50S ribosomal protein L6 /


分子量: 19568.926 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72I19
#32: タンパク質 50S ribosomal protein L9 /


分子量: 16436.205 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72GV5
#33: タンパク質 50S ribosomal protein L11 /


分子量: 15526.111 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P36238
#34: タンパク質 50S ribosomal protein L13 /


分子量: 18534.008 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72IN1
#35: タンパク質 50S ribosomal protein L14 /


分子量: 13309.586 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72I14, UniProt: P60558*PLUS
#36: タンパク質 50S ribosomal protein L15 /


分子量: 16319.142 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72I23
#37: タンパク質 50S ribosomal protein L16 /


分子量: 15977.909 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72I11
#38: タンパク質 50S ribosomal protein L17 /


分子量: 13750.148 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72I33
#39: タンパク質 50S ribosomal protein L18 /


分子量: 12639.845 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72I20
#40: タンパク質 50S ribosomal protein L19 /


分子量: 17217.867 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72JU9
#41: タンパク質 50S ribosomal protein L20 /


分子量: 13779.275 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72L76
#42: タンパク質 50S ribosomal protein L21 /


分子量: 11069.153 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72HR2
#43: タンパク質 50S ribosomal protein L22 /


分子量: 12808.055 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72I09
#44: タンパク質 50S ribosomal protein L23 /


分子量: 10759.808 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72I06
#45: タンパク質 50S ribosomal protein L24 /


分子量: 12085.611 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72I15, UniProt: Q56435*PLUS
#46: タンパク質 50S ribosomal protein L25 / / TL5 / GENERAL STRESS PROTEIN CTC


分子量: 23238.572 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72IA7
#47: タンパク質 50S ribosomal protein L27 /


分子量: 9501.061 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72HR3
#48: タンパク質 50S ribosomal protein L28 /


分子量: 11032.174 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72G84
#49: タンパク質 50S ribosomal protein L29 /


分子量: 8670.258 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72I12
#50: タンパク質 50S ribosomal protein L30 /


分子量: 6799.126 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72I22
#51: タンパク質 50S ribosomal protein L31 /


分子量: 11274.987 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72JR0
#52: タンパク質 50S ribosomal protein L32 /


分子量: 6734.104 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P62652
#53: タンパク質 50S ribosomal protein L33 /


分子量: 6632.896 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72GW3
#54: タンパク質・ペプチド 50S ribosomal protein L34 /


分子量: 6132.449 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: P80340
#55: タンパク質 50S ribosomal protein L35 /


分子量: 7506.178 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB27 / 参照: UniProt: Q72L77

-
非ポリマー , 2種, 2392分子

#56: 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: 2388 / 由来タイプ: 合成 / 式: Mg
#57: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Zn

-
詳細

配列の詳細E.COLI NUMBERING IS USED FOR 5S, 16S AND 23S RRNA. P- AND E-TRNA (TRNA FMET) HAVE NUMBERING ...E.COLI NUMBERING IS USED FOR 5S, 16S AND 23S RRNA. P- AND E-TRNA (TRNA FMET) HAVE NUMBERING ACCORDING TO THE CANONICAL YEAST TRNA PHE. RF2 AND RIBOSOMAL PROTEINS HAVE NUMBERING BASED ON THE PREDICTED SEQUENCE POSITION OF THE START METHIONINE (POSITION 1).

-
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: 3.45 Å3/Da / 溶媒含有率: 64 %
結晶化温度: 296 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7
詳細: 100 MM TRIS-OAC, 200 MM KSCN, 3.5-4.5 % (W/V) PEG20K, 4-9 % PEG200, DEOXY BIGCHAP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
溶液の組成
ID名称Crystal-IDSol-ID
1TRIS-OAC11
2KSCN11
3PEG20K11
4PEG20011
5DEOXY BIGCHAP11
6TRIS-OAC12
7KSCN12
8PEG20K12
9PEG20012
10DEOXY BIGCHAP12

-
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: APS / ビームライン: 23-ID-D / 波長: 0.9537
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2008年4月1日
詳細: SI(111) DOUBLE CRYSTAL MONOCHROMATOR. ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY
放射モノクロメーター: DOUBLE CRYSTAL CRYO-COOLED SI(111)
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: 0.9537 Å / 相対比: 1
反射解像度: 3→49.951 Å / Num. obs: 1148216 / % possible obs: 97.9 % / 冗長度: 16.8 % / Net I/σ(I): 8.8
反射 シェル解像度: 3→3.11 Å / 冗長度: 8.4 % / Mean I/σ(I) obs: 2.4 / % possible all: 89.9

-
解析

ソフトウェア
名称バージョン分類
PHENIX(phenix.refine)精密化
CNS1.2精密化
XDSデータ削減
XDSデータスケーリング
CNS1.2位相決定
精密化開始モデル: PDB ENTRIES 3D5A, 3D5B, 3D5C, 3D5D

3d5a
PDB 未公開エントリ

3d5b
PDB 未公開エントリ

3d5c
PDB 未公開エントリ

3d5d
PDB 未公開エントリ


解像度: 3→49.951 Å / SU ML: 0.72 / σ(F): 1.99 / 立体化学のターゲット値: ML
詳細: REFINEMENT WAS PERFORMED IN CNS v1.2 AND IN PHENIX. STATISTICS AS CALCULATED BY PHENIX.
Rfactor反射数%反射
Rfree0.3164 10481 0.91 %
Rwork0.2803 --
obs0.2806 1148216 97.34 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 26.922 Å2 / ksol: 0.184 e/Å3
精密化ステップサイクル: LAST / 解像度: 3→49.951 Å
タンパク質核酸リガンド溶媒全体
原子数21920 35826 528 0 58274
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11AA87040X-RAY DIFFRACTIONPOSITIONAL
12AB87040X-RAY DIFFRACTIONPOSITIONAL0.031
21AA51387X-RAY DIFFRACTIONPOSITIONAL
22AB51387X-RAY DIFFRACTIONPOSITIONAL0.023
31AA1854X-RAY DIFFRACTIONPOSITIONAL
32AB1854X-RAY DIFFRACTIONPOSITIONAL0.023
41AA1640X-RAY DIFFRACTIONPOSITIONAL
42AB1640X-RAY DIFFRACTIONPOSITIONAL0.008
51AA1994X-RAY DIFFRACTIONPOSITIONAL
52AB1994X-RAY DIFFRACTIONPOSITIONAL0.017
61AA882X-RAY DIFFRACTIONPOSITIONAL
62AB882X-RAY DIFFRACTIONPOSITIONAL0.009
71AA2239X-RAY DIFFRACTIONPOSITIONAL
72AB2239X-RAY DIFFRACTIONPOSITIONAL0.015
81AA1241X-RAY DIFFRACTIONPOSITIONAL
82AB1241X-RAY DIFFRACTIONPOSITIONAL0.015
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.03410.45293130.440232998X-RAY DIFFRACTION85
3.0341-3.06980.4193190.435234215X-RAY DIFFRACTION88
3.0698-3.10720.45863750.435434939X-RAY DIFFRACTION90
3.1072-3.14650.45463700.427735610X-RAY DIFFRACTION92
3.1465-3.18790.43313350.425436405X-RAY DIFFRACTION94
3.1879-3.23160.48012200.421936768X-RAY DIFFRACTION95
3.2316-3.27780.42893670.406236859X-RAY DIFFRACTION95
3.2778-3.32670.41853690.405137063X-RAY DIFFRACTION96
3.3267-3.37860.4363680.389437352X-RAY DIFFRACTION96
3.3786-3.4340.41893320.385137578X-RAY DIFFRACTION97
3.434-3.49320.41771060.380638045X-RAY DIFFRACTION98
3.4932-3.55670.40784110.369337989X-RAY DIFFRACTION98
3.5567-3.62510.41064080.347538304X-RAY DIFFRACTION99
3.6251-3.69910.36211860.337138693X-RAY DIFFRACTION99
3.6991-3.77950.34943310.323438799X-RAY DIFFRACTION100
3.7795-3.86740.35744110.307538626X-RAY DIFFRACTION100
3.8674-3.96410.34612170.292938909X-RAY DIFFRACTION100
3.9641-4.07120.32463750.268738781X-RAY DIFFRACTION100
4.0712-4.19090.30543870.251338721X-RAY DIFFRACTION100
4.1909-4.32610.28424170.235238861X-RAY DIFFRACTION100
4.3261-4.48060.2693790.221538862X-RAY DIFFRACTION100
4.4806-4.65990.25224010.208838881X-RAY DIFFRACTION100
4.6599-4.87180.25393710.196738892X-RAY DIFFRACTION100
4.8718-5.12840.24383980.181639013X-RAY DIFFRACTION100
5.1284-5.44940.22444010.16739020X-RAY DIFFRACTION100
5.4494-5.86950.23113760.161839149X-RAY DIFFRACTION100
5.8695-6.45910.21864080.162239135X-RAY DIFFRACTION100
6.4591-7.39120.21273680.165839340X-RAY DIFFRACTION100
7.3912-9.30230.22013700.185539527X-RAY DIFFRACTION100
9.3023-49.95820.27673920.255540401X-RAY DIFFRACTION100
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1861-0.11930.00910.43230.07740.1410.0481-0.03090.08280.15310.05140.1148-0.0137-0.00610.0085-0.06280.0121-0.1570.10410.0329-0.2903-18.7053136.4885167.2092
20.1244-0.03050.0670.676-0.15410.31780.01940.01480.0168-0.14810.10050.16740.0224-0.01380.4147-0.51580.0665-0.2575-0.02450.0129-0.3982-71.8307-57.26320.72
30.3677-0.15890.03340.1637-0.14910.26060.15040.0885-0.2297-0.3359-0.13460.44450.0585-0.234900.79250.1171-0.60930.6183-0.19981.1681-95.2572102.499567.6886
40.2-0.246-0.11220.16290.02230.24720.04950.0877-0.1334-0.222-0.02110.5833-0.3137-0.302600.73290.3892-0.39610.65970.09291.3514-147.102544.769-7.7089
50.19030.0162-0.07040.42450.1690.22490.02870.0534-0.0745-0.1682-0.0042-0.03070.03070.0434-00.30930.0476-0.14570.2389-0.01110.0901-13.063469.622895.1276
60.2142-0.08010.08690.5301-0.13720.2392-0.01490.09720.1063-0.3291-0.0546-0.0435-0.12420.093400.532-0.0827-0.17210.24610.15690.345-66.467816.8318-43.8649
70.0137-0.07350.0818-0.0685-0.0662-0.01870.04020.42980.1567-0.48520.34820.6758-0.2562-0.62190.00011.64830.2881-0.32891.62930.43311.4489-50.683194.211888.5494
80.0174-0.0781-0.0572-0.01030.0763-0.0537-0.0099-0.15020.39130.3458-0.260.6476-0.1556-0.4962-0.00011.60610.36170.20751.4826-0.46281.9397-101.017820.631281.323
90.02980.010.0222-0.0002-0.00190.01090.0584-0.1384-0.1173-0.0667-0.0450.05440.0106-0.1134-01.1685-0.40060.06421.8973-0.21611.8768-95.501566.3137164.1222
100.0716-0.03320.00750.0309-0.00120.02130.1508-0.03-0.0847-0.0635-0.02040.0797-0.09150.0443-01.90620.3297-0.10871.94190.03272.8444-150.3278-50.3791-48.511
110.0357-0.04330.01310.04890.00670.05640.009-0.0599-0.3602-0.1005-0.00750.05780.2204-0.020300.77290.0331-0.26850.7813-0.07871.0269-66.430290.9554120.2743
120.08760.0435-0.02580.0484-0.03160.0517-0.07010.14180.0166-0.1626-0.02020.0323-0.18840.0158-01.2090.1358-0.31550.9770.21531.5454-119.7495-7.8783-21.9081
130.05330.0066-0.06590.0644-0.00390.03930.07340.1994-0.0077-0.058-0.10040.0712-0.0083-0.22901.6475-0.1141-0.11581.98170.04651.8017-88.663463.0452123.7586
140.06380.0671-0.01030.049-0.02930.07910.03160.0043-0.0362-0.03910.0472-0.07110.09420.034402.22840.1471-0.08672.1189-0.06652.5313-142.7015-9.8299-49.482
150.01060.04090.09330.07880.19870.0666-0.03060.00910.0320.07290.0110.38740.0868-0.114200.3743-0.01030.18080.68720.14241.4655-115.2086144.3468166.3565
160.0047-0.0270.07590.0089-0.04770.06510.02310.1992-0.1159-0.29780.04410.19120.1133-0.040302.0332-0.275-0.23691.8106-0.07471.9047-65.744161.0225104.672
17-0.00480.00150.0077-0.00080.0024-0.0110.0088-0.03880.039-0.00880.0377-0.0195-0.0096-0.0389-0.00010.50040.1259-0.2190.67070.04770.6735-58.658895.701186.0149
180.0460.04070.03750.0445-0.11040.04970.0008-0.1199-0.1283-0.0742-0.07260.2266-0.0549-0.0542-00.3750.1137-0.18410.5865-0.06910.838-69.5446125.4477122.6163
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1070.03950.0610.01180.03190.00740.0961-0.02250.0456-0.00390.01390.06720.00910.10680.0153-01.20560.475-0.47991.05530.18381.3614-160.579770.6153-14.919
1080.0231-0.00580.01580.03120.0040.00460.09060.02550.0442-0.04880.03130.0616-0.02620.120900.73960.309-0.27090.6456-0.26780.8381-90.797534.122342.8111
1090.01570.014-0.03290.0443-0.02730.0460.1059-0.07550.1228-0.1862-0.10550.0315-0.11980.0801-00.8486-0.0529-0.43890.3950.15480.6731-94.582411.0596-46.0135
1100.0251-0.01320.0210.00010.00730.0068-0.0292-0.09290.08640.11470.06420.0818-0.0598-0.072100.73830.2709-0.24681.06580.23771.7819-169.158915.267916.6335
1110.0056-0.00870.01070.0074-0.0019-0.00460.0103-0.0258-0.01930.05890.00940.0519-0.0473-0.0185-00.75040.3595-0.2430.80090.04150.992-153.837944.9078-23.521
1120.0141-0.00060.00790.00830.0020.00530.0168-0.0593-0.0303-0.05050.1901-0.0593-0.0447-0.0304-00.5849-0.2198-0.4630.52550.00880.8201-34.295833.8983-2.548
1130.0109-0.00580.00520.0058-0.01730.00840.0511-0.02260.007-0.04780.06690.0034-0.03170.030.00011.27890.02880.07871.02150.41860.8481-52.784124.0309-87.2482
1140.0089-0.0132-0.0186-0.0014-0.0193-0.0151-0.09920.04040.0174-0.0071-0.0706-0.14240.02190.0978-00.83-0.16590.17570.97250.22450.9779-35.109421.406-36.8474
1150.00770.01170.00040.00880.00770.00250.07850.0060.0428-0.0110.07090.0209-0.0954-0.0475-00.6601-0.071-0.28240.5789-0.04230.9459-64.248350.275930.0922
1160.0115-0.00640.00390.01750.00050.0129-0.0270.0407-0.02650.017-0.0115-0.00790.0014-0.004801.15860.3427-0.35551.26990.10621.727-174.12299.7197-17.5695
1170.00310.00980.00780.0179-0.03380.00530.04730.00810.0219-0.08980.0838-0.0444-0.03960.0233-01.1932-0.04490.11930.85930.20880.9202-22.1101-10.4546-67.8263
1180.00240.00150.00020.00370.00140.00380.002-0.0034-0.0034-0.00370.02360.01130.0034-0.029301.00170.2276-0.17041.18480.03961.3088-166.469136.510710.4734
1190.0027-0.00370.00040.00130.00020.0017-0.0026-0.01130.0184-0.0069-0.00020.0053-0.01390.0048-01.25960.0727-0.12961.14130.01791.2316-131.3668151.685110.3825
1200.0025-00.00020.00180.00010.0022-0.0018-0.0217-0.00510.0241-0.0013-0.00190.00830.0068-01.35670.06390.03881.33160.13191.4432-182.78471.49740.4328
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1((chain BA) and not (resid 2093:2196 or resid 1051:1108))
2X-RAY DIFFRACTION2((chain DA) and not (resid 2093:2196 or resid 1051:1108))
3X-RAY DIFFRACTION3((chain AA and resid 925:1391))
4X-RAY DIFFRACTION4((chain CA and resid 925:1391))
5X-RAY DIFFRACTION5(chain AA and not resid 925:1391)
6X-RAY DIFFRACTION6(chain CA and not resid 925:1391)
7X-RAY DIFFRACTION7(chain BA and resid 2093:2196)
8X-RAY DIFFRACTION8(chain DA and resid 2093:2196)
9X-RAY DIFFRACTION9(chain BA and resid 1051:1108)
10X-RAY DIFFRACTION10(chain DA and resid 1051:1108)
11X-RAY DIFFRACTION11(chain AX and not resid 1:124)
12X-RAY DIFFRACTION12(chain CX and not resid 1:124)
13X-RAY DIFFRACTION13(chain AX and resid 1:124)
14X-RAY DIFFRACTION14(chain CX and resid 1:124)
15X-RAY DIFFRACTION15(chain BB)
16X-RAY DIFFRACTION16(chain AZ)
17X-RAY DIFFRACTION17(chain AV)
18X-RAY DIFFRACTION18(chain AY)
19X-RAY DIFFRACTION19(chain DB)
20X-RAY DIFFRACTION20(chain CZ)
21X-RAY DIFFRACTION21(chain CV)
22X-RAY DIFFRACTION22(chain CY)
23X-RAY DIFFRACTION23(chain BD)
24X-RAY DIFFRACTION24(chain BE)
25X-RAY DIFFRACTION25(chain BF)
26X-RAY DIFFRACTION26(chain BG)
27X-RAY DIFFRACTION27(chain BH)
28X-RAY DIFFRACTION28(chain BI)
29X-RAY DIFFRACTION29(chain BK)
30X-RAY DIFFRACTION30(chain BN)
31X-RAY DIFFRACTION31(chain BO)
32X-RAY DIFFRACTION32(chain BP)
33X-RAY DIFFRACTION33(chain BQ)
34X-RAY DIFFRACTION34(chain BR)
35X-RAY DIFFRACTION35(chain BS)
36X-RAY DIFFRACTION36(chain BT)
37X-RAY DIFFRACTION37(chain BU)
38X-RAY DIFFRACTION38(chain BV)
39X-RAY DIFFRACTION39(chain BW)
40X-RAY DIFFRACTION40(chain BX)
41X-RAY DIFFRACTION41(chain BY)
42X-RAY DIFFRACTION42(chain BZ)
43X-RAY DIFFRACTION43(chain B0)
44X-RAY DIFFRACTION44(chain B1)
45X-RAY DIFFRACTION45(chain B2)
46X-RAY DIFFRACTION46(chain B3)
47X-RAY DIFFRACTION47(chain B5)
48X-RAY DIFFRACTION48(chain B6)
49X-RAY DIFFRACTION49(chain B7)
50X-RAY DIFFRACTION50(chain B8)
51X-RAY DIFFRACTION51(chain AB)
52X-RAY DIFFRACTION52(chain AC)
53X-RAY DIFFRACTION53(chain AD)
54X-RAY DIFFRACTION54(chain AE)
55X-RAY DIFFRACTION55(chain AF)
56X-RAY DIFFRACTION56(chain AG)
57X-RAY DIFFRACTION57(chain AH)
58X-RAY DIFFRACTION58(chain AI)
59X-RAY DIFFRACTION59(chain AJ)
60X-RAY DIFFRACTION60(chain AK)
61X-RAY DIFFRACTION61(chain AL)
62X-RAY DIFFRACTION62(chain AM)
63X-RAY DIFFRACTION63(chain AN)
64X-RAY DIFFRACTION64(chain AO)
65X-RAY DIFFRACTION65(chain AP)
66X-RAY DIFFRACTION66(chain AQ)
67X-RAY DIFFRACTION67(chain AR)
68X-RAY DIFFRACTION68(chain AS)
69X-RAY DIFFRACTION69(chain AT)
70X-RAY DIFFRACTION70(chain AU)
71X-RAY DIFFRACTION71(chain DD)
72X-RAY DIFFRACTION72(chain DE)
73X-RAY DIFFRACTION73(chain DF)
74X-RAY DIFFRACTION74(chain DG)
75X-RAY DIFFRACTION75(chain DH)
76X-RAY DIFFRACTION76(chain DI)
77X-RAY DIFFRACTION77(chain DK)
78X-RAY DIFFRACTION78(chain DN)
79X-RAY DIFFRACTION79(chain DO)
80X-RAY DIFFRACTION80(chain DP)
81X-RAY DIFFRACTION81(chain DQ)
82X-RAY DIFFRACTION82(chain DR)
83X-RAY DIFFRACTION83(chain DS)
84X-RAY DIFFRACTION84(chain DT)
85X-RAY DIFFRACTION85(chain DU)
86X-RAY DIFFRACTION86(chain DV)
87X-RAY DIFFRACTION87(chain DW)
88X-RAY DIFFRACTION88(chain DX
89X-RAY DIFFRACTION89(chain DY)
90X-RAY DIFFRACTION90(chain DZ)
91X-RAY DIFFRACTION91(chain D0)
92X-RAY DIFFRACTION92(chain D1)
93X-RAY DIFFRACTION93(chain D2)
94X-RAY DIFFRACTION94(chain D3)
95X-RAY DIFFRACTION95(chain D5)
96X-RAY DIFFRACTION96(chain D6)
97X-RAY DIFFRACTION97(chain D7)
98X-RAY DIFFRACTION98(chain D8)
99X-RAY DIFFRACTION99(chain CB)
100X-RAY DIFFRACTION100(chain CC)
101X-RAY DIFFRACTION101(chain CD)
102X-RAY DIFFRACTION102(chain CE)
103X-RAY DIFFRACTION103(chain CF)
104X-RAY DIFFRACTION104(chain CG)
105X-RAY DIFFRACTION105(chain CH)
106X-RAY DIFFRACTION106(chain CI)
107X-RAY DIFFRACTION107(chain CJ)
108X-RAY DIFFRACTION108(chain CK)
109X-RAY DIFFRACTION109(chain CL)
110X-RAY DIFFRACTION110(chain CM)
111X-RAY DIFFRACTION111(chain CN)
112X-RAY DIFFRACTION112(chain CO)
113X-RAY DIFFRACTION113(chain CP)
114X-RAY DIFFRACTION114(chain CQ)
115X-RAY DIFFRACTION115(chain CR)
116X-RAY DIFFRACTION116(chain CS)
117X-RAY DIFFRACTION117(chain CT)
118X-RAY DIFFRACTION118(chain CU)
119X-RAY DIFFRACTION119(chain B4)
120X-RAY DIFFRACTION120(chain D4)

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万見について

-
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