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- PDB-4v6d: Crystal structure of the E. coli 70S ribosome in an intermediate ... -

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基本情報

登録情報
データベース: PDB / ID: 4v6d
タイトルCrystal structure of the E. coli 70S ribosome in an intermediate state of ratcheting
要素
  • (16S rRNA) x 2
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • (5S rRNA) x 2
  • 23S rRNA
  • P-site tRNA ASL fragment
  • messenger RNA
キーワードRIBOSOME / ribosome structure / protein-RNA complex / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / Antibiotic resistance / Repressor / Transcription / Transcription regulation / Transcription termination / Translation regulation / tRNA-binding / Methylation / Endonuclease / Hydrolase / Nuclease
機能・相同性
機能・相同性情報


stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity ...stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / translational termination / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / regulation of mRNA stability / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / ribosome assembly / transcription elongation factor complex / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / response to reactive oxygen species / DNA endonuclease activity / transcription antitermination / regulation of cell growth / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / ribosome biogenesis / large ribosomal subunit / regulation of translation / transferase activity / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
類似検索 - 分子機能
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L11, bacterial-type / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L11, bacterial-type / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / 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, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L17 signature. / 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, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / 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 L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / 30S ribosomal protein S17 / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L30, bacterial-type
類似検索 - ドメイン・相同性
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / 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 uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25
類似検索 - 構成要素
生物種Escherichia coli K-12 (大腸菌)
Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 解像度: 3.814 Å
データ登録者Zhang, W. / Dunkle, J.A. / Cate, J.H.D.
引用ジャーナル: Science / 年: 2009
タイトル: Structures of the ribosome in intermediate States of ratcheting.
著者: Zhang, W. / Dunkle, J.A. / Cate, J.H.
履歴
登録2009年6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: 3I1Q, 3I1R, 3I1S, 3I1T
改定 1.12014年12月10日Group: Other
改定 1.22024年10月30日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
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.pdbx_dist_value / _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

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
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 S21
AA: 16S rRNA
AV: P-site tRNA ASL fragment
AW: messenger RNA
BA: 23S rRNA
BB: 5S rRNA
BC: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BE: 50S ribosomal protein L4
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BH: 50S ribosomal protein L9
BI: 50S ribosomal protein L11
BJ: 50S ribosomal protein L13
BK: 50S ribosomal protein L14
BL: 50S ribosomal protein L15
BM: 50S ribosomal protein L16
BN: 50S ribosomal protein L17
BO: 50S ribosomal protein L18
BP: 50S ribosomal protein L19
BQ: 50S ribosomal protein L20
BR: 50S ribosomal protein L21
BS: 50S ribosomal protein L22
BT: 50S ribosomal protein L23
BU: 50S ribosomal protein L24
BV: 50S ribosomal protein L25
BW: 50S ribosomal protein L27
BX: 50S ribosomal protein L28
BY: 50S ribosomal protein L29
BZ: 50S ribosomal protein L30
B0: 50S ribosomal protein L32
B1: 50S ribosomal protein L33
B2: 50S ribosomal protein L34
B3: 50S ribosomal protein L35
B4: 50S ribosomal protein L36
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 S21
CA: 16S rRNA
CV: P-site tRNA ASL fragment
CW: messenger RNA
DC: 50S ribosomal protein L2
DD: 50S ribosomal protein L3
DE: 50S ribosomal protein L4
DF: 50S ribosomal protein L5
DG: 50S ribosomal protein L6
DH: 50S ribosomal protein L9
DI: 50S ribosomal protein L11
DJ: 50S ribosomal protein L13
DK: 50S ribosomal protein L14
DL: 50S ribosomal protein L15
DM: 50S ribosomal protein L16
DN: 50S ribosomal protein L17
DO: 50S ribosomal protein L18
DP: 50S ribosomal protein L19
DQ: 50S ribosomal protein L20
DR: 50S ribosomal protein L21
DS: 50S ribosomal protein L22
DT: 50S ribosomal protein L23
DU: 50S ribosomal protein L24
DV: 50S ribosomal protein L25
DW: 50S ribosomal protein L27
DX: 50S ribosomal protein L28
DY: 50S ribosomal protein L29
DZ: 50S ribosomal protein L30
D0: 50S ribosomal protein L32
D1: 50S ribosomal protein L33
D2: 50S ribosomal protein L34
D3: 50S ribosomal protein L35
D4: 50S ribosomal protein L36
DA: 23S rRNA
DB: 5S rRNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)4,308,870473
ポリマ－4,299,917108
非ポリマー8,954365
水30,9501718
1
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 S21
AA: 16S rRNA
AV: P-site tRNA ASL fragment
AW: messenger RNA
BA: 23S rRNA
BB: 5S rRNA
BC: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BE: 50S ribosomal protein L4
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BH: 50S ribosomal protein L9
BI: 50S ribosomal protein L11
BJ: 50S ribosomal protein L13
BK: 50S ribosomal protein L14
BL: 50S ribosomal protein L15
BM: 50S ribosomal protein L16
BN: 50S ribosomal protein L17
BO: 50S ribosomal protein L18
BP: 50S ribosomal protein L19
BQ: 50S ribosomal protein L20
BR: 50S ribosomal protein L21
BS: 50S ribosomal protein L22
BT: 50S ribosomal protein L23
BU: 50S ribosomal protein L24
BV: 50S ribosomal protein L25
BW: 50S ribosomal protein L27
BX: 50S ribosomal protein L28
BY: 50S ribosomal protein L29
BZ: 50S ribosomal protein L30
B0: 50S ribosomal protein L32
B1: 50S ribosomal protein L33
B2: 50S ribosomal protein L34
B3: 50S ribosomal protein L35
B4: 50S ribosomal protein L36
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,155,143239
ポリマ－2,150,60554
非ポリマー4,538185
水34219
タイプ名称対称操作数
identity operation1_555x,y,z1
2
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 S21
CA: 16S rRNA
CV: P-site tRNA ASL fragment
CW: messenger RNA
DC: 50S ribosomal protein L2
DD: 50S ribosomal protein L3
DE: 50S ribosomal protein L4
DF: 50S ribosomal protein L5
DG: 50S ribosomal protein L6
DH: 50S ribosomal protein L9
DI: 50S ribosomal protein L11
DJ: 50S ribosomal protein L13
DK: 50S ribosomal protein L14
DL: 50S ribosomal protein L15
DM: 50S ribosomal protein L16
DN: 50S ribosomal protein L17
DO: 50S ribosomal protein L18
DP: 50S ribosomal protein L19
DQ: 50S ribosomal protein L20
DR: 50S ribosomal protein L21
DS: 50S ribosomal protein L22
DT: 50S ribosomal protein L23
DU: 50S ribosomal protein L24
DV: 50S ribosomal protein L25
DW: 50S ribosomal protein L27
DX: 50S ribosomal protein L28
DY: 50S ribosomal protein L29
DZ: 50S ribosomal protein L30
D0: 50S ribosomal protein L32
D1: 50S ribosomal protein L33
D2: 50S ribosomal protein L34
D3: 50S ribosomal protein L35
D4: 50S ribosomal protein L36
DA: 23S rRNA
DB: 5S rRNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,153,727234
ポリマ－2,149,31154
非ポリマー4,416180
水37821
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)210.7200, 435.0700, 628.7300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

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

#1: タンパク質 30S ribosomal protein S2


分子量: 26781.670 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7V0
#2: タンパク質 30S ribosomal protein S3


分子量: 26031.316 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7V3
#3: タンパク質 30S ribosomal protein S4


分子量: 23514.199 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7V8
#4: タンパク質 30S ribosomal protein S5


分子量: 17629.398 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7W1
#5: タンパク質 30S ribosomal protein S6 / 30S ribosomal protein S6 / fully modified isoform / 30S ribosomal protein S6 / non-modified isoform


分子量: 15727.512 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P02358
#6: タンパク質 30S ribosomal protein S7


分子量: 20055.156 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P02359
#7: タンパク質 30S ribosomal protein S8


分子量: 14146.557 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7W7
#8: タンパク質 30S ribosomal protein S9


分子量: 14886.270 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7X3
#9: タンパク質 30S ribosomal protein S10


分子量: 11755.597 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7R5
#10: タンパク質 30S ribosomal protein S11


分子量: 13870.975 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7R9
#11: タンパク質 30S ribosomal protein S12


分子量: 13768.157 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7S3
#12: タンパク質 30S ribosomal protein S13


分子量: 13128.467 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7S9
#13: タンパク質 30S ribosomal protein S14


分子量: 11606.560 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0AG59
#14: タンパク質 30S ribosomal protein S15


分子量: 10290.816 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0ADZ4
#15: タンパク質 30S ribosomal protein S16


分子量: 9207.572 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7T3
#16: タンパク質 30S ribosomal protein S17


分子量: 9724.491 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0AG63
#17: タンパク質 30S ribosomal protein S18


分子量: 9005.472 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7T7
#18: タンパク質 30S ribosomal protein S19


分子量: 10455.355 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7U3
#19: タンパク質 30S ribosomal protein S20


分子量: 9708.464 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7U7
#20: タンパク質 30S ribosomal protein S21


分子量: 8524.039 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P68679

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RNA鎖 , 7種, 10分子 AAAVCVAWCWBADABBCADB

#21: RNA鎖 16S rRNA


分子量: 496892.375 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌)
#22: RNA鎖 P-site tRNA ASL fragment


分子量: 5402.276 Da / 分子数: 2 / Fragment: RNA hairpin / 由来タイプ: 合成
#23: RNA鎖 messenger RNA


分子量: 1854.118 Da / 分子数: 2 / 由来タイプ: 合成
#24: RNA鎖 23S rRNA


分子量: 941306.188 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌)
#25: RNA鎖 5S rRNA


分子量: 38177.762 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌)
#55: RNA鎖 16S rRNA


分子量: 495927.719 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌)
#56: RNA鎖 5S rRNA


分子量: 37848.555 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌)

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50S ribosomal protein ... , 29種, 58分子 BCDCBDDDBEDEBFDFBGDGBHDHBIDIBJDJBKDKBLDLBMDMBNDNBODOBPDPBQDQ...

#26: タンパク質 50S ribosomal protein L2


分子量: 29923.619 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P60422
#27: タンパク質 50S ribosomal protein L3


分子量: 22277.535 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P60438
#28: タンパク質 50S ribosomal protein L4


分子量: 22121.566 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P60723
#29: タンパク質 50S ribosomal protein L5


分子量: 20333.611 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P62399
#30: タンパク質 50S ribosomal protein L6


分子量: 18932.791 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0AG55
#31: タンパク質 50S ribosomal protein L9


分子量: 15789.020 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7R1
#32: タンパク質 50S ribosomal protein L11


分子量: 14894.362 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7J7
#33: タンパク質 50S ribosomal protein L13


分子量: 16050.606 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0AA10
#34: タンパク質 50S ribosomal protein L14


分子量: 13565.067 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0ADY3
#35: タンパク質 50S ribosomal protein L15


分子量: 15008.471 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P02413
#36: タンパク質 50S ribosomal protein L16


分子量: 15312.269 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0ADY7
#37: タンパク質 50S ribosomal protein L17


分子量: 14393.657 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0AG44
#38: タンパク質 50S ribosomal protein L18


分子量: 12794.668 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0C018
#39: タンパク質 50S ribosomal protein L19


分子量: 13159.278 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7K6
#40: タンパク質 50S ribosomal protein L20


分子量: 13528.024 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7L3
#41: タンパク質 50S ribosomal protein L21


分子量: 11586.374 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0AG48
#42: タンパク質 50S ribosomal protein L22


分子量: 12253.359 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P61175
#43: タンパク質 50S ribosomal protein L23


分子量: 11222.160 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0ADZ0
#44: タンパク質 50S ribosomal protein L24


分子量: 11339.250 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P60624
#45: タンパク質 50S ribosomal protein L25


分子量: 10713.465 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P68919
#46: タンパク質 50S ribosomal protein L27


分子量: 9146.540 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7L8
#47: タンパク質 50S ribosomal protein L28


分子量: 9027.551 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7M2
#48: タンパク質 50S ribosomal protein L29


分子量: 7286.464 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7M6
#49: タンパク質 50S ribosomal protein L30


分子量: 6554.820 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0AG51
#50: タンパク質 50S ribosomal protein L32


分子量: 6463.445 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7N4
#51: タンパク質 50S ribosomal protein L33


分子量: 6388.631 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7N9
#52: タンパク質・ペプチド 50S ribosomal protein L34


分子量: 5397.463 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7P5
#53: タンパク質 50S ribosomal protein L35 / Ribosomal protein A


分子量: 7313.032 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7Q1
#54: タンパク質・ペプチド 50S ribosomal protein L36 / Ribosomal protein B


分子量: 4377.390 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0A7Q6

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非ポリマー , 3種, 2083分子

#57: 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: 363 / 由来タイプ: 合成 / 式: Mg
#58: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn
#59: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1718 / 由来タイプ: 天然 / 式: H2O

-
詳細

Has protein modificationY

-
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: 3.35 Å3/Da / 溶媒含有率: 63.3 %
結晶化温度: 291 K / 手法: マイクロバッチ法 / pH: 7
詳細: 4% PEG 8000, 4% MPD, 3.8 mM MgCl2, 380 mM NH4Cl, 5.5 mM putrescine, 5 mM spermidine, pH 7.0, microbatch, temperature 291K
溶液の組成
ID名称Crystal-IDSol-ID
1PEG 800011
2MPD11
3MgCl211
4NH4Cl11
5putrescine11
6spermidine11
7PEG 800012
8MPD12
9MgCl212
10NH4Cl12
11putrescine12
12spermidine12

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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: 24-ID-C / 波長: 0.97918 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2008年11月15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: 0.97918 Å / 相対比: 1
反射解像度: 3.8→100 Å / Num. obs: 438691 / % possible obs: 78.8 % / 冗長度: 2.2 % / Rmerge(I) obs: 0.111 / Χ2: 1.587 / Net I/σ(I): 9.6
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.8-3.871.50.56158741.266157.4
3.87-3.941.60.499160641.418158.3
3.94-4.011.60.466166121.265160.1
4.01-4.091.70.423172371.289162.4
4.09-4.181.70.405181831.252165.6
4.18-4.281.80.361191171.254169.2
4.28-4.391.80.329202091.217173.2
4.39-4.511.90.301211511.238176.4
4.51-4.6420.267219211.295179.2
4.64-4.792.10.244224751.415181
4.79-4.962.10.221228161.425182.4
4.96-5.162.10.197232671.465183.8
5.16-5.392.20.18236141.481184.9
5.39-5.682.20.167240051.605186.4
5.68-6.032.30.158245401.681188.1
6.03-6.52.40.154249491.781189.6
6.5-7.152.80.126258771.734192.6
7.15-8.1930.094267701.757195.3
8.19-10.3130.069269921.847195.6
10.31-10030.043270181.833193.2

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解析

ソフトウェア
名称バージョン分類NB
SCALEPACKデータスケーリング
PHENIX精密化
PDB_EXTRACT3.006データ抽出
PHASER位相決定
DENZOデータ削減
精密化解像度: 3.814→75.71 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: -0 / σ(F): 1.33 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.253 8839 2.02 %RANDOM
Rwork0.207 ---
obs0.208 438250 78.63 %-
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: 49.632 Å2 / ksol: 0.252 e/Å3
原子変位パラメータBiso max: 334.42 Å2 / Biso mean: 138.745 Å2 / Biso min: 35.39 Å2
Baniso -1Baniso -2Baniso -3
1-3.597 Å20 Å20 Å2
2---10.627 Å20 Å2
3---7.029 Å2
精密化ステップサイクル: LAST / 解像度: 3.814→75.71 Å
タンパク質核酸リガンド溶媒全体
原子数18543 33380 43 208 52174
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.007309580
X-RAY DIFFRACTIONf_angle_d1.549463850
X-RAY DIFFRACTIONf_chiral_restr0.0858828
X-RAY DIFFRACTIONf_plane_restr0.00524764
X-RAY DIFFRACTIONf_dihedral_angle_d28.127161432
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 (%)
3.814-3.8570.351890.39784997354
3.857-3.9020.352250.296104921071758
3.902-3.950.3292230.272104991072258
3.95-40.321960.277107601095659
4-4.0520.3182270.269110671129461
4.052-4.1080.3332110.257113201153163
4.108-4.1670.2992510.259117751202665
4.167-4.2290.282500.248121811243167
4.229-4.2950.2922640.245126141287870
4.295-4.3650.2782620.241130641332672
4.365-4.4410.2572680.237135271379575
4.441-4.5210.2712930.231139571425077
4.521-4.6080.2772790.22142261450579
4.608-4.7020.2782990.215145671486680
4.702-4.8050.2543470.213146711501881
4.805-4.9160.2442910.216148871517882
4.916-5.0390.2772940.205151261542083
5.039-5.1750.2593230.192152121553584
5.175-5.3280.2353100.192153711568185
5.328-5.50.2433090.19155701587986
5.5-5.6960.2523220.187157961611887
5.696-5.9240.2463390.184159101624988
5.924-6.1940.2533600.181162831664389
6.194-6.520.2413640.186163121667690
6.52-6.9280.2383470.179168071715492
6.928-7.4630.233540.171172661762094
7.463-8.2130.2123730.17175271790096
8.213-9.3990.2213320.177176481798096
9.399-11.8350.2033770.167176511802895
11.835-75.7250.2173600.207175411790192
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)
11.8283-0.452-0.06971.05070.04230.55180.07040.50690.2482-0.5732-0.152-0.2474-0.2848-0.002-00.88110.08580.14540.45640.23640.6419-63.904614.1155-74.1227
20.0232-0.00660.05840.07220.0150.0444-0.0028-0.14450.04160.06320.0646-0.3202-0.28080.139200.74150.1585-0.06570.3196-0.00280.872-87.10637.0739-28.2881
30.0295-0.04370.00950.0266-0.01480.04070.02630.26960.2816-0.32910.1368-0.2495-0.43790.337301.82480.52110.11862.27130.40862.2362-98.178961.5537-34.7188
40.06510.00120.00320.0318-0.00470.0263-0.02570.01810.0915-0.02630.0537-0.0712-0.2952-0.0101.90590.3530.22972.59810.61272.0772-79.681460.6366-41.6295
50.07480.0265-0.02960.16230.01910.10490.2438-0.44410.11160.23410.15180.1559-0.1670.152202.90050.0973-0.231.9390.30693.8779-86.839485.8161-9.6659
60.02760.00790.0090.04650.00590.028-0.0143-0.11080.01310.0587-0.04880.01080.0376-0.060302.11260.07380.08382.03330.0372.4474-118.787285.3143-8.8843
71.6977-0.4094-0.26930.91670.09330.8611-0.0218-0.1387-0.04560.20160.14880.3374-0.1865-0.329601.04240.56420.06161.01560.06870.8753-148.147243.8574-3.5581
80.15560.0161-0.00780.08810.10170.11570.13450.35040.3799-0.44520.23460.5928-0.3951-0.622601.98670.6763-0.46272.026-0.32221.9211-168.361528.5492-50.3668
90.6715-0.1050.06940.702-0.10190.5904-0.0821-0.36950.43760.34260.1081-0.3515-0.52040.185400.97660.1642-0.26290.4652-0.3170.9887-65.44938.6122-0.0539
10-0.03640.19770.18660.61-0.21430.6524-0.14650.3543-0.0849-0.1628-0.1466-0.20770.0288-0.1196-00.4345-0.02860.07280.40180.01170.5046-57.2337-5.8248-40.1999
111.2801-0.14430.46570.67520.13731.2882-0.1092-0.2003-0.35520.18750.164-0.1040.38580.3277-00.97940.15540.11790.566-0.11470.6594-30.258232.5243106.7884
120.03030.0797-0.03620.09570.04610.0438-0.1223-0.0171-0.1205-0.03040.0778-0.27190.00510.140300.9408-0.1805-0.05340.4723-0.19240.4019-42.106179.918678.8185
130.01960.02050.0290.0429-0.02390.04040.13190.4058-0.1803-0.10550.148-0.06040.050.180401.3388-0.1321-0.55080.9043-0.29290.9833-51.960472.391855.5072
140.02540.0015-0.00230.0199-0.02890.0227-0.03570.0327-0.2605-0.1561-0.1162-0.17940.24110.1739-01.3712-0.4559-0.08141.055-0.40911.2967-35.280762.229560.5669
150.0708-0.0008-0.03450.0664-0.02680.0932-0.06090.43230.3906-0.312-0.2365-0.2672-0.33790.217502.1392-0.36540.46462.1633-0.44670.7218-31.858990.646329.7999
160.02380.0069-0.0010.021-0.0010.02360.01280.08620.05330.04450.01010.1152-0.0469-0.101701.9536-0.088-0.01941.6689-0.08081.3344-62.66797.384225.2637
171.7174-0.1850.11991.02140.13240.72740.02380.03090.2515-0.3169-0.08740.4606-0.2544-0.439701.4269-0.1262-0.34771.0095-0.0670.8037-96.7853112.445659.904
180.13090.0339-0.03370.1039-0.09850.0947-0.00610.3724-0.4321-0.2793-0.33190.69690.0838-0.6585-02.0146-0.5544-0.28312.13360.00682.0937-126.32970.895375.0931
190.4466-0.1962-0.04961.01260.15770.55030.02990.20510.0822-0.61260.1961-0.4606-0.32420.4744-01.1225-0.44840.20490.9499-0.33560.4898-16.1321104.490779.708
200.01950.3489-0.36320.34730.10790.5198-0.1275-0.1971-0.29010.04090.2129-0.06830.30620.244701.13210.0728-0.14160.8631-0.14260.612-23.931466.9192127.162
210.49520.0178-0.10590.44570.01670.441-0.0134-0.12330.00170.1829-0.0086-0.0866-0.01430.0677-0-0.39790.0341-0.1259-0.0986-0.11970.059-66.236-60.087915.911
22-0.09140.06790.10260.1276-0.3835-0.22530.19170.36752.6206-0.9716-0.0133-0.4497-2.54780.0747-02.1202-0.1729-0.37081.73430.58733.5935-140.1367-50.122-62.9105
230.06070.02820.01670.03090.0230.0033-0.10110.27340.0153-0.41640.09060.1151-0.0526-0.133800.58340.077-0.01740.8803-0.00680.6586-104.1937-4.0765-1.3213
240.1283-0.1276-0.08910.00410.07990.054-0.1862-0.67720.66880.5180.38511.458-1.322-1.969-02.90970.18630.01082.3588-0.11642.2558-95.769217.163480.7797
250.05710.00160.00360.03190.00010.04750.0030.29740.3308-0.1293-0.0956-0.0075-0.3307-0.0329-02.4829-0.05330.06841.9650.01722.4873-149.3341-27.5176-10.987
260.0182-0.08650.06630.1472-0.02610.1276-0.06070.2271.2293-0.16720.063-0.2131-1.5210.754-00.9092-0.12120.06191.46460.04211.5157-166.3051-23.822416.9125
270.4104-0.2845-0.18940.3199-0.08220.23910.1066-0.09310.03450.0029-0.25730.30690.1898-0.1859-00.10180.00170.14770.7012-0.22970.8309-175.0319-54.40331.0753
280.0764-0.1029-0.02090.0772-0.04220.1895-0.30860.6124-0.0709-1.46860.11630.30790.4128-0.1695-0-0.73230.0590.00870.5212-0.13080.5117-144.1992-80.2997-7.4528
290.1255-0.0078-0.02550.0646-0.05090.14170.0541-0.30230.43290.191-0.09940.0132-0.46440.0564-03.1634-0.0952-0.13932.777-0.1382.806-65.016420.0022122.6139
300.374-0.0665-0.18110.49860.05530.80890.0338-0.31310.07170.0310.1951-0.143-0.24560.532400.8454-0.2949-0.02221.0779-0.23950.2423-29.3466128.4379174.782
310.07670.06510.00940.07980.18250.11610.20161.3654-0.4078-1.5475-0.0795-0.19590.65960.44102.792-0.2215-0.1323.5124-0.33962.9744-117.467971.9981153.7128
320.01840.0032-0.01480.0064-0.03240.07270.070.0411-0.3372-0.0901-0.03160.12740.4133-0.123501.3644-0.36130.05960.8165-0.1350.5992-60.7698113.9858114.2741
330.0459-0.04840.05610.10750.0220.07130.02230.44790.2517-0.0144-0.21790.6396-0.2786-1.1115-02.0573-0.2580.41822.055-0.02251.2578-29.1778190.389792.0505
340.0157-0.0052-0.00530.0143-0.00180.01410.00260.0895-0.0447-0.0186-0.06560.0360.0305-0.084801.78120.2265-0.04531.7696-0.33541.5409-110.4021124.1205136.8154
350.0929-0.01640.06040.18020.0140.1744-0.27070.67870.2112-0.6072-0.15090.3153-0.0984-0.126202.7110.13480.36012.870.15153.1956-121.0938152.2128118.7309
360.2071-0.1233-0.01740.0599-0.02090.12280.2357-0.05140.6821-0.27680.00790.0953-0.5429-0.28201.82530.32070.02611.74310.09871.6513-128.1805170.2351147.5084
370.0594-0.07880.04580.03160.0420.1539-0.22210.3377-0.9530.2111-0.22991.47550.7422-1.1627-01.0971-0.06690.16131.6385-0.22711.3319-113.4726128.1624180.3553
380.11990.0130.06470.13590.05940.06810.18750.59290.2457-0.4007-0.0208-0.081-0.18310.0529-02.85470.05370.36492.92570.09592.360811.1573227.208588.9552
390.0193-0.02050.0060.0360.02550.0220.0594-0.091-0.19020.1405-0.10590.18140.3913-0.2744-00.98310.39270.10950.86510.00260.983-119.776917.0490.7703
400.01790.02190.00580.0251-0.00890.04790.0328-0.18990.17620.16290.03760.19590.0527-0.2055-01.1805-0.1051-0.1040.7749-0.15070.6525-72.8301115.185890.8007
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1((chain AA and (resid 2:8 or resid 27:557)) or (chain AD and resid 1:205) or (chain AP and resid 1:82) or (chain AT and resid 2:86) or (chain AL and resid 22:123) or (chain ZQ and (resid 299 or resid 315 or resid 362 or resid 417 or resid 509 o1
2X-RAY DIFFRACTION2((chain AA and (resid 9:26 or resid 558:562 or resid 564:566 or resid 914:925 or resid 1391:1396)) or (chain AL and resid 1:21) or (chain ZQ and (resid 21 or resid 560)))
3X-RAY DIFFRACTION3(chain AE and resid 9:73)
4X-RAY DIFFRACTION4(chain AE and resid 74:149)
5X-RAY DIFFRACTION5(chain AB and (resid 8:107 or resid 147:225))
6X-RAY DIFFRACTION6(chain AB and resid 108:146)
7X-RAY DIFFRACTION7((chain AA and (resid 926:986 or resid 1048:1390)) or (chain AC and resid 1:206) or (chain AG and resid 1:151) or (chain AI and resid 3:129) or (chain AJ and resid 5:102) or (chain AM and resid 1:114) or (chain AN and resid 1:100) or (chain A7
8X-RAY DIFFRACTION8(chain AA and resid 987:1047)
9X-RAY DIFFRACTION9((chain AA and (resid 563 or resid 567:913 or resid 1496:1530)) or (chain AF and resid 1:100) or (chain AH and resid 1:129) or (chain AK and resid 12:128) or (chain AO and resid 1:88) or (chain AR and resid 19:73) or (chain AU and resid 3:53)9
10X-RAY DIFFRACTION10((chain AA and resid 1397:1495) or (chain ZQ and (resid 1417 or resid 8201)))
11X-RAY DIFFRACTION11((chain CA and (resid 2:8 or resid 27:557)) or (chain CD and resid 1:205) or (chain CP and resid 1:82) or (chain CT and resid 2:86) or (chain CL and resid 22:123) or (chain ZU and (resid 299 or resid 315 or resid 362 or resid 417 or resid 509 o11
12X-RAY DIFFRACTION12((chain CA and (resid 9:26 or resid 558:562 or resid 564:566 or resid 914:925 or resid 1391:1396)) or (chain CL and resid 1:21) or (chain ZU and (resid 21 or resid 560)))
13X-RAY DIFFRACTION13(chain CE and resid 9:73)
14X-RAY DIFFRACTION14(chain CE and resid 74:149)
15X-RAY DIFFRACTION15(chain CB and (resid 8:107 or resid 147:225))
16X-RAY DIFFRACTION16(chain CB and resid 108:146)
17X-RAY DIFFRACTION17((chain CA and (resid 926:986 or resid 1048:1390)) or (chain CC and resid 1:206) or (chain CG and resid 1:151) or (chain CI and resid 3:129) or (chain CJ and resid 5:102) or (chain CM and resid 1:114) or (chain CN and resid 1:100) or (chain C17
18X-RAY DIFFRACTION18(chain CA and resid 987:1047)
19X-RAY DIFFRACTION19((chain CA and (resid 563 or resid 567:913 or resid 1496:1530)) or (chain CF and resid 1:100) or (chain CH and resid 1:129) or (chain CK and resid 12:128) or (chain CO and resid 1:88) or (chain CR and resid 19:73) or (chain CU and resid 3:53)19
20X-RAY DIFFRACTION20((chain CA and resid 1397:1495) or (chain ZU and (resid 1417 or resid 8201)))
21X-RAY DIFFRACTION21((chain BA and (resid 1:876 or resid 902:1038 or resid 1116:1905 or resid 1930:2092 or resid 2198:2296 or resid 2322:2903)) or (chain BC and resid 1:271) or (chain BS and resid 1:110) or (chain BT and resid 1:93) or (chain BU and resid 1:102) o21
22X-RAY DIFFRACTION22((chain BA and resid 1039:1115) or (chain BI and resid 1:141))
23X-RAY DIFFRACTION23(chain BA and resid 1906:1929)
24X-RAY DIFFRACTION24(chain BA and resid 2093:2197)
25X-RAY DIFFRACTION25(chain BA and resid 877:901)
26X-RAY DIFFRACTION26((chain BA and resid 2297:2321) or (chain BF and resid 1:177) or (chain ZR and resid 2304))
27X-RAY DIFFRACTION27((chain BB and (resid 2:69 or resid 108:119)) or (chain BO and resid 2:117))
28X-RAY DIFFRACTION28((chain BB and resid 70:107) or (chain BV and resid 1:94) or (chain ZR and resid 6095:6100))
29X-RAY DIFFRACTION29(chain BH and resid 49:149)
30X-RAY DIFFRACTION30((chain DA and (resid 1:876 or resid 902:1038 or resid 1116:1905 or resid 1930:2092 or resid 2198:2296 or resid 2322:2903)) or (chain DC and resid 1:271) or (chain DS and resid 1:110) or (chain DT and resid 1:93) or (chain DU and resid 1:102) o30
31X-RAY DIFFRACTION31((chain DA and resid 1039:1115) or (chain DI and resid 1:141))
32X-RAY DIFFRACTION32(chain DA and resid 1906:1929)
33X-RAY DIFFRACTION33(chain DA and resid 2093:2197)
34X-RAY DIFFRACTION34(chain DA and resid 877:901)
35X-RAY DIFFRACTION35((chain DA and resid 2297:2321) or (chain DF and resid 1:178) or (chain ZT and resid 2304))
36X-RAY DIFFRACTION36((chain DB and (resid 2:69 or resid 108:119)) or (chain DO and resid 2:117))
37X-RAY DIFFRACTION37((chain DB and resid 70:107) or (chain DV and resid 1:94) or (chain ZT and resid 6095:6100))
38X-RAY DIFFRACTION38(chain DH and resid 49:149)
39X-RAY DIFFRACTION39(chain I or chain J)
40X-RAY DIFFRACTION40(chain K or chain L)

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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