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- PDB-5j5b: Structure of the WT E coli ribosome bound to tetracycline -

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基本情報

登録情報
データベース: PDB / ID: 5j5b
タイトルStructure of the WT E coli ribosome bound to tetracycline
要素
  • (23S rRNA) x 2
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 30
  • 16S rRNA
  • 5S rRNA
キーワードRIBOSOME/ANTIBIOTIC / ribosome / escherichia coli / tetracycline / sq171 / RIBOSOME-ANTIBIOTIC complex
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 / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / 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 L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / 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 L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / 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 L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / 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 S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein S9, bacterial/plastid
類似検索 - ドメイン・相同性
ACETIC ACID / GUANINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 1,4-DIAMINOBUTANE / SPERMIDINE / TETRACYCLINE / : / : / RNA ...ACETIC ACID / GUANINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 1,4-DIAMINOBUTANE / SPERMIDINE / TETRACYCLINE / : / : / 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 uL10 / 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 (大腸菌)
手法X線回折 / シンクロトロン / 解像度: 2.8 Å
データ登録者Cocozaki, A. / Ferguson, A.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2016
タイトル: Resistance mutations generate divergent antibiotic susceptibility profiles against translation inhibitors.
著者: Cocozaki, A.I. / Altman, R.B. / Huang, J. / Buurman, E.T. / Kazmirski, S.L. / Doig, P. / Prince, D.B. / Blanchard, S.C. / Cate, J.H. / Ferguson, A.D.
履歴
登録2016年4月1日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年7月27日Provider: repository / タイプ: Initial release
改定 1.12016年8月3日Group: Database references
改定 2.02018年8月15日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
カテゴリ: citation / entity_poly ...citation / entity_poly / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_oper_list.symmetry_operation
改定 2.12025年2月12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 / 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
改定 2.22025年3月19日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_atom.pdbx_aromatic_flag ..._chem_comp_atom.atom_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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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
AA: 16S rRNA
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
C1: 50S ribosomal protein L32
C2: 50S ribosomal protein L33
C3: 50S ribosomal protein L34
C4: 50S ribosomal protein L35
C5: 50S ribosomal protein L36
C0: 50S ribosomal protein L30
BA: 16S rRNA
BB: 30S ribosomal protein S2
BC: 30S ribosomal protein S3
BD: 30S ribosomal protein S4
BE: 30S ribosomal protein S5
BF: 30S ribosomal protein S6
BG: 30S ribosomal protein S7
BH: 30S ribosomal protein S8
BI: 30S ribosomal protein S9
BJ: 30S ribosomal protein S10
BK: 30S ribosomal protein S11
BL: 30S ribosomal protein S12
BM: 30S ribosomal protein S13
BN: 30S ribosomal protein S14
BO: 30S ribosomal protein S15
BP: 30S ribosomal protein S16
BQ: 30S ribosomal protein S17
BR: 30S ribosomal protein S18
BS: 30S ribosomal protein S19
BT: 30S ribosomal protein S20
BU: 30S ribosomal protein S21
D1: 50S ribosomal protein L32
D2: 50S ribosomal protein L33
D3: 50S ribosomal protein L34
D4: 50S ribosomal protein L35
D5: 50S ribosomal protein L36
D0: 50S ribosomal protein L30
CB: 5S rRNA
CC: 50S ribosomal protein L2
CD: 50S ribosomal protein L3
CA: 23S rRNA
DC: 50S ribosomal protein L2
DD: 50S ribosomal protein L3
CE: 50S ribosomal protein L4
CF: 50S ribosomal protein L5
CG: 50S ribosomal protein L6
CH: 50S ribosomal protein L9
CJ: 50S ribosomal protein L11
CK: 50S ribosomal protein L13
CL: 50S ribosomal protein L14
CM: 50S ribosomal protein L15
CN: 50S ribosomal protein L16
CO: 50S ribosomal protein L17
CP: 50S ribosomal protein L18
CQ: 50S ribosomal protein L19
CR: 50S ribosomal protein L20
CS: 50S ribosomal protein L21
CT: 50S ribosomal protein L22
CU: 50S ribosomal protein L23
CV: 50S ribosomal protein L24
CW: 50S ribosomal protein L25
CX: 50S ribosomal protein L27
CY: 50S ribosomal protein L28
CZ: 50S ribosomal protein L29
DE: 50S ribosomal protein L4
DF: 50S ribosomal protein L5
DG: 50S ribosomal protein L6
DH: 50S ribosomal protein L9
DJ: 50S ribosomal protein L11
DK: 50S ribosomal protein L13
DL: 50S ribosomal protein L14
DM: 50S ribosomal protein L15
DN: 50S ribosomal protein L16
DO: 50S ribosomal protein L17
DP: 50S ribosomal protein L18
DQ: 50S ribosomal protein L19
DR: 50S ribosomal protein L20
DS: 50S ribosomal protein L21
DT: 50S ribosomal protein L22
DU: 50S ribosomal protein L23
DV: 50S ribosomal protein L24
DW: 50S ribosomal protein L25
DX: 50S ribosomal protein L27
DY: 50S ribosomal protein L28
DZ: 50S ribosomal protein L29
DI: 50S ribosomal protein L10
DB: 5S rRNA
DA: 23S rRNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)4,271,830659
ポリマ－4,250,147105
非ポリマー21,683554
水139,5447746
1
AA: 16S rRNA
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
D1: 50S ribosomal protein L32
D2: 50S ribosomal protein L33
D3: 50S ribosomal protein L34
D4: 50S ribosomal protein L35
D5: 50S ribosomal protein L36
D0: 50S ribosomal protein L30
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
DJ: 50S ribosomal protein L11
DK: 50S ribosomal protein L13
DL: 50S ribosomal protein L14
DM: 50S ribosomal protein L15
DN: 50S ribosomal protein L16
DO: 50S ribosomal protein L17
DP: 50S ribosomal protein L18
DQ: 50S ribosomal protein L19
DR: 50S ribosomal protein L20
DS: 50S ribosomal protein L21
DT: 50S ribosomal protein L22
DU: 50S ribosomal protein L23
DV: 50S ribosomal protein L24
DW: 50S ribosomal protein L25
DX: 50S ribosomal protein L27
DY: 50S ribosomal protein L28
DZ: 50S ribosomal protein L29
DI: 50S ribosomal protein L10
DB: 5S rRNA
DA: 23S rRNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,148,428402
ポリマ－2,132,35953
非ポリマー16,070349
水86548
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C1: 50S ribosomal protein L32
C2: 50S ribosomal protein L33
C3: 50S ribosomal protein L34
C4: 50S ribosomal protein L35
C5: 50S ribosomal protein L36
C0: 50S ribosomal protein L30
BA: 16S rRNA
BB: 30S ribosomal protein S2
BC: 30S ribosomal protein S3
BD: 30S ribosomal protein S4
BE: 30S ribosomal protein S5
BF: 30S ribosomal protein S6
BG: 30S ribosomal protein S7
BH: 30S ribosomal protein S8
BI: 30S ribosomal protein S9
BJ: 30S ribosomal protein S10
BK: 30S ribosomal protein S11
BL: 30S ribosomal protein S12
BM: 30S ribosomal protein S13
BN: 30S ribosomal protein S14
BO: 30S ribosomal protein S15
BP: 30S ribosomal protein S16
BQ: 30S ribosomal protein S17
BR: 30S ribosomal protein S18
BS: 30S ribosomal protein S19
BT: 30S ribosomal protein S20
BU: 30S ribosomal protein S21
CB: 5S rRNA
CC: 50S ribosomal protein L2
CD: 50S ribosomal protein L3
CA: 23S rRNA
CE: 50S ribosomal protein L4
CF: 50S ribosomal protein L5
CG: 50S ribosomal protein L6
CH: 50S ribosomal protein L9
CJ: 50S ribosomal protein L11
CK: 50S ribosomal protein L13
CL: 50S ribosomal protein L14
CM: 50S ribosomal protein L15
CN: 50S ribosomal protein L16
CO: 50S ribosomal protein L17
CP: 50S ribosomal protein L18
CQ: 50S ribosomal protein L19
CR: 50S ribosomal protein L20
CS: 50S ribosomal protein L21
CT: 50S ribosomal protein L22
CU: 50S ribosomal protein L23
CV: 50S ribosomal protein L24
CW: 50S ribosomal protein L25
CX: 50S ribosomal protein L27
CY: 50S ribosomal protein L28
CZ: 50S ribosomal protein L29
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,123,402257
ポリマ－2,117,78852
非ポリマー5,614205
水46826
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)212.310, 434.580, 624.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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要素

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RNA鎖 , 4種, 6分子 AABACBDBCADA

#1: RNA鎖 16S rRNA


分子量: 497404.969 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: GenBank: 731469900
#28: RNA鎖 5S rRNA


分子量: 38790.090 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: GenBank: 939731527
#31: RNA鎖 23S rRNA


分子量: 941809.562 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: GenBank: 939731527
#54: RNA鎖 23S rRNA


分子量: 941811.562 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: GenBank: 939731527

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

#2: タンパク質 30S ribosomal protein S2


分子量: 24971.764 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7V0
#3: タンパク質 30S ribosomal protein S3


分子量: 23078.785 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7V3
#4: タンパク質 30S ribosomal protein S4


分子量: 23383.002 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7V8
#5: タンパク質 30S ribosomal protein S5


分子量: 16361.878 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7W1
#6: タンパク質 30S ribosomal protein S6


分子量: 12326.251 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P02358
#7: タンパク質 30S ribosomal protein S7


分子量: 16861.523 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P02359
#8: タンパク質 30S ribosomal protein S8


分子量: 14015.361 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7W7
#9: タンパク質 30S ribosomal protein S9


分子量: 14554.882 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7X3
#10: タンパク質 30S ribosomal protein S10


分子量: 11325.117 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7R5
#11: タンパク質 30S ribosomal protein S11


分子量: 12487.200 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7R9
#12: タンパク質 30S ribosomal protein S12


分子量: 13683.053 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7S3
#13: タンパク質 30S ribosomal protein S13


分子量: 12625.753 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7S9
#14: タンパク質 30S ribosomal protein S14


分子量: 11475.364 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0AG59
#15: タンパク質 30S ribosomal protein S15


分子量: 10159.621 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0ADZ4
#16: 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 (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7T3
#17: タンパク質 30S ribosomal protein S17


分子量: 9263.946 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0AG63
#18: タンパク質 30S ribosomal protein S18


分子量: 6466.477 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7T7
#19: タンパク質 30S ribosomal protein S19


分子量: 9057.626 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7U3
#20: タンパク質 30S ribosomal protein S20


分子量: 9577.268 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7U7
#21: タンパク質 30S ribosomal protein S21


分子量: 6629.744 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P68679

+
50S ribosomal protein ... , 30種, 59分子 C1D1C2D2C3D3C4D4C5D5C0D0CCDCCDDDCEDECFDFCGDGCHDHCJDJCKDKCLDL...

#22: タンパク質 50S ribosomal protein L32


分子量: 6332.249 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7N4
#23: タンパク質 50S ribosomal protein L33


分子量: 5928.000 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7N9
#24: 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 (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7P5
#25: タンパク質 50S ribosomal protein L35 / Ribosomal protein A


分子量: 7181.835 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7Q1
#26: 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 (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7Q6
#27: タンパク質 50S ribosomal protein L30


分子量: 6423.625 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0AG51
#29: タンパク質 50S ribosomal protein L2


分子量: 29663.244 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P60422
#30: タンパク質 50S ribosomal protein L3


分子量: 22291.562 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P60438
#32: 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 (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P60723
#33: タンパク質 50S ribosomal protein L5


分子量: 20073.234 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P62399
#34: タンパク質 50S ribosomal protein L6


分子量: 18801.598 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0AG55
#35: 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 (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7R1
#36: タンパク質 50S ribosomal protein L11


分子量: 14020.303 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7J7
#37: 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 (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0AA10
#38: 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 (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0ADY3
#39: 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 (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P02413
#40: タンパク質 50S ribosomal protein L16


分子量: 15327.261 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0ADY7
#41: タンパク質 50S ribosomal protein L17


分子量: 14193.465 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0AG44
#42: 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 (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0C018
#43: タンパク質 50S ribosomal protein L19


分子量: 13028.082 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7K6
#44: タンパク質 50S ribosomal protein L20


分子量: 13396.828 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7L3
#45: 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 (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0AG48
#46: 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 (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P61175
#47: タンパク質 50S ribosomal protein L23


分子量: 10546.472 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0ADZ0
#48: タンパク質 50S ribosomal protein L24


分子量: 11078.874 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P60624
#49: 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 (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P68919
#50: タンパク質 50S ribosomal protein L27


分子量: 8275.498 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7L8
#51: タンパク質 50S ribosomal protein L28


分子量: 8896.354 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7M2
#52: タンパク質 50S ribosomal protein L29


分子量: 7155.267 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7M6
#53: タンパク質 50S ribosomal protein L10 / 50S ribosomal protein L8


分子量: 14568.748 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (strain K12) (大腸菌) / 株: K12 / 参照: UniProt: P0A7J3

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非ポリマー , 15種, 8300分子

#55: 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: 469 / 由来タイプ: 合成 / 式: Mg
#56: 化合物
ChemComp-PG4 / TETRAETHYLENE GLYCOL / テトラエチレングリコ-ル


分子量: 194.226 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C8H18O5 / コメント: 沈殿剤*YM
#57: 化合物
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / (S)-2-メチル-2,4-ペンタンジオ-ル


分子量: 118.174 Da / 分子数: 14 / 由来タイプ: 合成 / 式: C6H14O2 / コメント: 沈殿剤*YM
#58: 化合物
ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE / プトレシン


分子量: 88.151 Da / 分子数: 16 / 由来タイプ: 合成 / 式: C4H12N2
#59: 化合物 ChemComp-TAC / TETRACYCLINE / テトラサイクリン


分子量: 444.435 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C22H24N2O8 / コメント: 薬剤, 抗生剤*YM
#60: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Zn
#61: 化合物
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 11 / 由来タイプ: 合成 / 式: C4H10O3
#62: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 12 / 由来タイプ: 合成 / 式: C2H6O2
#63: 化合物
ChemComp-PGE / TRIETHYLENE GLYCOL / トリエチレングリコ-ル


分子量: 150.173 Da / 分子数: 9 / 由来タイプ: 合成 / 式: C6H14O4
#64: 化合物
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / スペルミジン


分子量: 145.246 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C7H19N3
#65: 化合物 ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / ペンタエチレングリコ-ル


分子量: 238.278 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H22O6 / コメント: 沈殿剤*YM
#66: 化合物 ChemComp-ACY / ACETIC ACID / 酢酸


分子量: 60.052 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C2H4O2
#67: 化合物 ChemComp-GUN / GUANINE / グアニン


分子量: 151.126 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C5H5N5O
#68: 化合物 ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / トリス(ヒドロキシメチル)メチルアンモニウム


分子量: 122.143 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C4H12NO3 / コメント: pH緩衝剤*YM
#69: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 7746 / 由来タイプ: 天然 / 式: H2O

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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: 3.39 Å3/Da / 溶媒含有率: 63.77 %
結晶化温度: 291 K / 手法: マイクロバッチ法
詳細: PEG 8000, Spermidine, Putrescine, Ammonium Chloride, Magnesium Chloride, MES pH 6.5

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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: 17-ID / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2014年4月25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 Å / 相対比: 1
反射解像度: 2.8→48.16 Å / Num. obs: 1291300 / % possible obs: 92.1 % / 冗長度: 4.5 % / Net I/σ(I): 188.6

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解析

ソフトウェア
名称バージョン分類
Aimlessデータスケーリング
BUSTER-TNT2.11.6精密化
PDB_EXTRACT3.2データ抽出
XDSデータ削減
BUSTER位相決定
精密化解像度: 2.8→48.16 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.893 / 交差検証法: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.321
Rfactor反射数%反射Selection details
Rfree0.219 4734 -RANDOM
Rwork0.209 ---
obs0.209 36007 85.7 %-
原子変位パラメータBiso max: 299.33 Å2 / Biso min: 6.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.9568 Å20 Å20 Å2
2--5.9265 Å20 Å2
3----6.8833 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
精密化ステップサイクル: final / 解像度: 2.8→48.16 Å
タンパク質核酸リガンド溶媒全体
原子数90649 195374 3682 7746 297451
Biso mean--157.71 63.2 -
残基数----20589
拘束条件
Refine-IDタイプ数Restraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d80764SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes2047HARMONIC2
X-RAY DIFFRACTIONt_gen_planes23405HARMONIC5
X-RAY DIFFRACTIONt_it311602HARMONIC20
X-RAY DIFFRACTIONt_nbd41SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion48422SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance1774HARMONIC1
X-RAY DIFFRACTIONt_utility_angle3169HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact321225SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d311602HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg465710HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion21.51
LS精密化 シェル解像度: 2.8→2.87 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.343 130 0.36 %
Rwork0.336 35877 -
all-36007 -
obs--35.03 %
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)
10.0188-0.1577-0.06660.2304-0.11140-0.04230.02210.02550.00310.05130.0082-0.02160.0205-0.009-0.18430.03590.0016-0.17710.1520.23-88.365124.9936-35.6167
20.25270.03020.10360.0491-0.091300.12740.0351-0.13690.1161-0.0020.0708-0.13950.041-0.12540.2375-0.152-0.109-0.27170.0696-0.0932-46.132277.208786.3778
30.051-0.14681.19761.4197-0.53890-0.0016-0.01110.00930.0054-0.0004-0.0106-0.0029-0.00460.0020.02840.0484-0.0209-0.06240.04850.0555-92.476685.5604-19.2965
40.15640.32450.320500.39410.92920.0010.00830.00340.00120.00110.0010.00530.0023-0.00210.0623-0.0277-0.01590.0217-0.019-0.0262-36.666191.455926.1707
50-0.35590.02271.1468-2.33460-0.00290.0171-0.0171-0.01740.0079-0.0045-0.0047-0.0026-0.005-0.04780.07370.0221-0.04990.11340.0729-140.77452.6795-37.7674
60.46550.76360.71280.8577-0.7160.1819-0.00090.0056-0.00180.00060.00170.0124-0.0095-0.0058-0.00080.0132-0.0568-0.0231-0.00110.01990.0347-91.17780.280547.8274
70.0117-2.6763-0.29550.9276-2.56740.0010.00450.01720.0043-0.0159-0.00890.0052-0.0095-0.01740.00440.03850.1416-0.0827-0.0370.15030.0201-95.15244.1621-80.1374
80.57350.11540.86141.63540.52260.00040.00410.0259-0.0426-0.0074-0.018-0.0327-0.0159-0.00720.01390.0611-0.0759-0.1252-0.1341-0.07380.0605-53.479534.290265.9232
90.7121-0.9057-0.62291.418-2.30080.6079-0.0023-0.0028-0.0031-0.0142-0.00420.0241-0.0220.00680.00650.00680.0709-0.0169-0.04980.12710.055-86.957657.4667-44.415
100.0837-0.21291.22410.7451.35230.0585-0.0020.0078-0.021-0.0068-0.0018-0.02390.00770.010.00380.0809-0.0719-0.1057-0.0234-0.02250.0039-41.207668.188455.9229
110.22640.48710.0090.56940.99920.2715-0.001-0.00510.00510.0004-0.0021-0.00210.00010.01170.00310.0357-0.0224-0.0204-0.0265-0.03460.024-48.133944.14735.832
120.45480.8137-0.39650.3705-0.49370-0.00160.00090.00910.00110.0009-0.0007-0.00090.01220.00070.0026-0.0570.0076-0.03340.04280.02219.1672141.342173.9312
130.2804-0.7527-0.6380.6079-0.54830.5040.0017-0.01170.00710.0054-0.00180.00550.0019-0.00680.00010.02070.02840.02290.01640.00790.0194-131.714449.352930.857
140.28630.17610.33240.31120.03770.18170.0007-0.00080.00320.0015-0.00060.0031-0.00120.001-0.00010.0079-0.0006-0.0071-0.0003-0.00020.0137-76.3984147.827254.2667
150.12040.5352-0.11050.6356-0.546200.00030.00110.00730.00690.0013-0.0018-0.01650.0032-0.00150.0006-0.0336-0.001-0.03290.07380.0595-54.20461.6814-37.5139
160.1495-0.2884-0.00790.60640.28370.41230.00070.0047-0.0105-0.0026-0.0012-0.010.00280.00440.00050.0359-0.005-0.0197-0.0221-0.01460.0368-6.685369.169357.2201
170.48410.148-1.16250.340.201500.0023-0.01680.00130.0073-0.0058-0.0025-0.0188-0.00850.00350.00670.0480.03610.01070.00850.036-152.546967.263614.2823
180.57270.22730.11740.1388-0.16320.0466-0.0009-0.00230.002-0.00030.00190.0056-0.00090.0002-0.0010.0042-0.0011-0.02570.00270.0190.0156-94.553133.13532.1242
190.63110.1957-1.81680.3845-2.36690.0016-0.0005-0.0002-0.0002-0.0031-0.00350.003-0.0144-0.01990.0039-0.01210.0520.0245-0.00210.06780.0439-162.848564.1046-20.131
2000.47410.22640.6919-0.424900.00080.0055-0.00250.002-0.00260.0009-0.0017-0.00150.00180.0077-0.0075-0.00910.00390.01070.0141-108.527399.936732.7049
210.0117-1.7491-0.41410.2841-0.29040.32270.0034-0.02060.01130.012-0.0061-0.0004-0.0055-0.00260.00260.02940.05810.01140.0086-0.01180.0213-93.25435.690137.8149
220-0.04150.42140.49420.16360.24880.00120.00330.0250.0018-0.00920.0052-0.0022-0.01840.0080.0248-0.0420.0145-0.01850.00020.0278-36.0661151.555374.206
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540.39860.55590.00480.0922-0.37320.0001-0.00150.00310.0015-0.0056-0.0020.0004-0.0056-0.00420.0035-0.0404-0.0197-0.05650.03980.03120.0216-114.7545-66.4347-44.111
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560.1405-0.0146-0.01290.04950.00670.0306-0.0227-0.00730.08540.02860.0025-0.01620.0141-0.01670.0202-0.16250.0049-0.0447-0.06090.00550.1501-69.3945-53.978517.308
570.8707-0.8383-0.1080.3919-0.93210.4638-0.0016-0.0106-0.00930.00280.00890.01140.0038-0.0044-0.0074-0.00590.0209-0.00080.01190.03940.0083-124.0466155.136154.8997
581.4441-0.7768-0.60490.84950.58610.2810.04370.0854-0.0126-0.01-0.07870.16930.07750.03050.035-0.28810.02960.04130.02520.11650.2325-163.7164-61.843516.0314
590.12611.77810.78440.26361.05560.12330.0094-0.04020.00080.0020.0108-0.0201-0.00240.0156-0.02020.0439-0.10690.01720.0234-0.0492-0.0782-1.2932138.2219117.525
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630.25140.5768-0.05660.29440.6170.14590.0007-0.00530.0089-0.00010.0060.0037-0.0096-0.0039-0.00670.0261-0.02570.01070.0113-0.04220.0053-31.6962183.6216205.6177
640.26050.0380.10070.5576-0.46350.7258-0.0195-0.0785-0.015-0.00790.0190.0337-0.0050.00770.0005-0.05150.04610.0140.05910.0779-0.0118-72.6858-97.195863.321
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700.0110.49320.23490-0.28330.75740.0013-0.0148-0.01390.01190.00470.0106-0.0044-0.0044-0.00590.009-0.0341-0.0214-0.0141-0.0279-0.0054-63.79228.9108108.2055
710.0248-0.0319-0.0650-0.11530.01430.00020.0010.00040.00050.00010.00040.0025-0.0009-0.00030.00250-0.00030.00460.00190.0034-119.996763.3711137.0416
720-0.2346-0.14220.2089-0.28480-0.00060.00010.0014-0.0018-0.00070-0.00190.00070.00130.00310.0038-0.0003-0.0010.00460.0096-145.3713-36.1826-71.1646
730.1610.2829-0.45080.1199-0.3590.64930.0021-0.0149-0.0010.00010.00250.00680.00240.0045-0.00470.0266-0.00290.01450.04030.03550.0038-68.847997.9076213.3799
740.70590.1578-0.26760.0745-0.14840.14270.00220.0676-0.0316-0.0083-0.011-0.01450.00920.00680.0088-0.1392-0.06-0.00850.0915-0.05210.0687-87.5453-104.3431-28.2659
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780.22980.0532-0.01210.0725-0.12570.2045-0.0088-0.0363-0.00230.0317-0.02170.0122-0.02860.00820.0304-0.04820.03610.05710.0487-0.0088-0.0096-100.9354-75.167563.0076
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850.3685-0.73040.11740.5078-0.2630.4736-0.00130.00460.00020.0030.0040.00080.001-0.0032-0.00260.02870.022-0.00280.0220.02760.0056-17.828554.2748167.017
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880.48250.03480.21990.24290.35350.1285-0.0078-0.0072-0.0473-0.0078-0.02150.01590.03920.04330.0293-0.1225-0.0541-0.02880.03360.05710.1012-88.6268-109.11232.6606
890.26480.51360.11290.02120.28680.4202-0.0002-0.01190.00270.0028-0.00090.009-0.00370.00040.00110.0211-0.01220.00890.02640.0023-0.0058-69.1792138.4089229.064
900.41970.07420.04020.68840.69920.2434-0.00260.0088-0.05050.02770.01210.00490.0294-0.0005-0.0095-0.06090.01870.0053-0.03320.0380.1095-93.427-122.340310.4945
910.46310.17890.1260.2810.09710.4020.0003-0.0007-0.00550.00320.0017-0.0017-0.00170.0007-0.0020.0216-0.0085-0.01510.0351-0.01-0.0068-11.5992117.2194212.737
921.10450.2478-0.52890.40070.40260.0155-0.00010.0053-0.0299-0.00890.0048-0.02840.02440.0032-0.0047-0.17180.0512-0.03080.05540.04030.1216-37.8332-94.07994.1218
930.12020.17090.39420.30790.44990.59740.0002-0.0011-0.00230.00020.0009-0.0007-0.0001-0.0003-0.00110.0039-0.0162-0.01420.0195-0.01840.007932.9957140.8994181.8074
940.3757-0.37710.84320.8777-0.47020.043-0.00290.0094-0.00030.01530.0014-0.0019-0.00040.00950.0015-0.0662-0.0326-0.13620.0094-0.00290.0534-6.3778-59.122239.2558
950.38780.2027-0.31630.08120.12050.5527-0.0009-0.00390.0007-0.0012-0.002-0.0017-0.00210.00160.00290.0129-0.0115-0.00910.0156-0.01720.005610.4276165.6267223.7625
960.7241-1.00970.65150-0.41790.0996-0.0025-0.005-0.017-0.02240.0139-0.0184-0.00740.0119-0.0114-0.02780.0568-0.05420.04080.0466-0.0077-25.3416-106.731455.3749
970.27710.1999-0.13730.3054-0.0990.30690.00070.0016-0.0001-0.0019-0.001-0.00180.0002-0.00040.00030.0022-0.00760.00740.01650.01470.0185-121.8933122.3417180.019
980.98820.12620.18920.46260.29020.57690.00040.0165-0.0006-0.0160.00620.00070.00350.0009-0.0066-0.1017-0.0453-0.07050.03350.00270.0684-149.8152-82.775-15.8374
990.075-0.149-0.17260.213-0.45740.29640.00020.00070.00170.0005-0.00160.002-0.00320.00030.00130.0180.00580.01780.00730.00510.0103-96.8344163.8961162.8526
1000.58550.0728-0.39260.5730.16880-0.0054-0.0104-0.00580.01350.00540.02360.0102-0.00040.0001-0.08240.04310.06870.0238-0.01940.0691-138.3158-64.868430.8303
1010.09860.4081-0.58830.5941.45530.3405-0.0016-0.00020.0008-0.00150.003-0.0042-0.00770.0118-0.00140.0225-0.06170.02810.0198-0.05140.0219-9.3272178.7764135.9788
1020.8609-0.3074-0.04670.32840.70640.1048-0.0027-0.02040.00220.00850-0.01350.00580.00950.0027-0.0069-0.0381-0.04210.005-0.10890.0199-64.6554-25.278368.3152
1030.0960.11850.27670.02750.1540.21790.0004-0.0008-0.0001-0.0007-0.00030.00040.0013-0.0002-0.00010.0086-0.012-0.01030.0095-0.0090.003235.8241163.0943191.2426
1040.4167-0.70570.7970-0.05280.05510.00020.0044-0.0028-0.0004-0.0059-0.0134-0.00040.00450.0058-0.01340.0248-0.08280.02140.01380.0023-6.9559-70.253760.7386
1050.70620.23970.25550-0.76170.09150.0013-0.0071-0.0049-0.0138-0.0011-0.0056-0.0077-0.0042-0.0002-0.01620.0105-0.03250.02810.04990.0057-155.0775-70.8242-76.5636
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|2209 }A1 - 2209
2X-RAY DIFFRACTION2{ B|2 - B|1986 }B2 - 1986
3X-RAY DIFFRACTION3{ A|2304 - A|2601 }A2304 - 2601
4X-RAY DIFFRACTION4{ B|2304 - B|2527 }B2304 - 2527
5X-RAY DIFFRACTION5{ A|2602 - A|2906 }A2602 - 2906
6X-RAY DIFFRACTION6{ B|2602 - B|2807 }B2602 - 2807
7X-RAY DIFFRACTION7{ A|3002 - A|3302 }A3002 - 3302
8X-RAY DIFFRACTION8{ B|3002 - B|3312 }B3002 - 3312
9X-RAY DIFFRACTION9{ A|3410 - A|3605 }A3410 - 3605
10X-RAY DIFFRACTION10{ B|3410 - B|3601 }B3410 - 3601
11X-RAY DIFFRACTION11{ A|3701 - A|3901 }A3701 - 3901
12X-RAY DIFFRACTION12{ B|3701 - B|3902 }B3701 - 3902
13X-RAY DIFFRACTION13{ A|4002 - A|4201 }A4002 - 4201
14X-RAY DIFFRACTION14{ B|4002 - B|4152 }B4002 - 4152
15X-RAY DIFFRACTION15{ A|4202 - A|4401 }A4202 - 4401
16X-RAY DIFFRACTION16{ B|4202 - B|4330 }B4202 - 4330
17X-RAY DIFFRACTION17{ A|4404 - A|4530 }A4404 - 4530
18X-RAY DIFFRACTION18{ B|4404 - B|4530 }B4404 - 4530
19X-RAY DIFFRACTION19{ A|4604 - A|4802 }A4604 - 4802
20X-RAY DIFFRACTION20{ B|4605 - B|4702 }B4605 - 4702
21X-RAY DIFFRACTION21{ A|4813 - A|5006 }A4813 - 5006
22X-RAY DIFFRACTION22{ B|4813 - B|4929 }B4813 - 4929
23X-RAY DIFFRACTION23{ A|5102 - A|5410 }A5102 - 5410
24X-RAY DIFFRACTION24{ B|5102 - B|5305 }B5102 - 5305
25X-RAY DIFFRACTION25{ A|5502 - A|5804 }A5502 - 5804
26X-RAY DIFFRACTION26{ B|5502 - B|5615 }B5502 - 5615
27X-RAY DIFFRACTION27{ A|5902 - A|6106 }A5902 - 6106
28X-RAY DIFFRACTION28{ B|5902 - B|6103 }B5902 - 6103
29X-RAY DIFFRACTION29{ A|6202 - A|6302 }A6202 - 6302
30X-RAY DIFFRACTION30{ B|6202 - B|6301 }B6202 - 6301
31X-RAY DIFFRACTION31{ A|6401 - A|6502 }A6401 - 6502
32X-RAY DIFFRACTION32{ B|6401 - B|6503 }B6401 - 6503
33X-RAY DIFFRACTION33{ A|6504 - A|6583 }A6504 - 6583
34X-RAY DIFFRACTION34{ B|6504 - B|6583 }B6504 - 6583
35X-RAY DIFFRACTION35{ A|6620 - A|6674 }A6620 - 6674
36X-RAY DIFFRACTION36{ B|6620 - B|6674 }B6620 - 6674
37X-RAY DIFFRACTION37{ A|6703 - A|6801 }A6703 - 6801
38X-RAY DIFFRACTION38{ B|6703 - B|6781 }B6703 - 6781
39X-RAY DIFFRACTION39{ A|6802 - A|6902 }A6802 - 6902
40X-RAY DIFFRACTION40{ B|6803 - B|6905 }B6803 - 6905
41X-RAY DIFFRACTION41{ A|7002 - A|7102 }A7002 - 7102
42X-RAY DIFFRACTION42{ B|7002 - B|7102 }B7002 - 7102
43X-RAY DIFFRACTION43{ A|7202 - A|7259 }A7202 - 7259
44X-RAY DIFFRACTION44{ B|7202 - B|7425 }B7202 - 7425
45X-RAY DIFFRACTION45{ A|7502 - A|7557 }A7502 - 7557
46X-RAY DIFFRACTION46{ B|7502 - B|7747 }B7502 - 7747
47X-RAY DIFFRACTION47{ A|7804 - A|7853 }A7804 - 7853
48X-RAY DIFFRACTION48{ B|7804 - B|7909 }B7804 - 7909
49X-RAY DIFFRACTION49{ A|8001 - A|8202 }A8001 - 8202
50X-RAY DIFFRACTION50{ B|8001 - B|8225 }B8001 - 8225
51X-RAY DIFFRACTION51{ A|8302 - A|8401 }A8302 - 8401
52X-RAY DIFFRACTION52{ B|8302 - B|8438 }B8302 - 8438
53X-RAY DIFFRACTION53{ A|8501 - A|8601 }A8501 - 8601
54X-RAY DIFFRACTION54{ B|8501 - B|8714 }B8501 - 8714
55X-RAY DIFFRACTION55{ C|1 - C|3892 }C1 - 3892
56X-RAY DIFFRACTION56{ D|1 - D|8115 }D1 - 8115
57X-RAY DIFFRACTION57{ C|8202 - C|8513 }C8202 - 8513
58X-RAY DIFFRACTION58{ D|8201 - D|8709 }D8201 - 8709
59X-RAY DIFFRACTION59{ C|8802 - C|9108 }C8802 - 9108
60X-RAY DIFFRACTION60{ D|8802 - D|9206 }D8802 - 9206
61X-RAY DIFFRACTION61{ C|9301 - C|9606 }C9301 - 9606
62X-RAY DIFFRACTION62{ D|9301 - D|9803 }D9301 - 9803
63X-RAY DIFFRACTION63{ E|1 - E|306 }E1 - 306
64X-RAY DIFFRACTION64{ F|1 - F|462 }F1 - 462
65X-RAY DIFFRACTION65{ E|502 - E|678 }E502 - 678
66X-RAY DIFFRACTION66{ F|502 - F|714 }F502 - 714
67X-RAY DIFFRACTION67{ E|802 - E|977 }E802 - 977
68X-RAY DIFFRACTION68{ F|802 - F|1006 }F802 - 1006
69X-RAY DIFFRACTION69{ E|1101 - E|1249 }E1101 - 1249
70X-RAY DIFFRACTION70{ F|1101 - F|1302 }F1101 - 1302
71X-RAY DIFFRACTION71{ E|1308 - E|1441 }E1308 - 1441
72X-RAY DIFFRACTION72{ F|1308 - F|1441 }F1308 - 1441
73X-RAY DIFFRACTION73{ E|1501 - E|1701 }E1501 - 1701
74X-RAY DIFFRACTION74{ F|1501 - F|1859 }F1501 - 1859
75X-RAY DIFFRACTION75{ E|1901 - E|2101 }E1901 - 2101
76X-RAY DIFFRACTION76{ F|1901 - F|2245 }F1901 - 2245
77X-RAY DIFFRACTION77{ E|2301 - E|2605 }E2301 - 2605
78X-RAY DIFFRACTION78{ F|2301 - F|2667 }F2301 - 2667
79X-RAY DIFFRACTION79{ E|2701 - E|2836 }E2701 - 2836
80X-RAY DIFFRACTION80{ F|2701 - F|3074 }F2701 - 3074
81X-RAY DIFFRACTION81{ E|3101 - E|3301 }E3101 - 3301
82X-RAY DIFFRACTION82{ F|3101 - F|3342 }F3101 - 3342
83X-RAY DIFFRACTION83{ E|3402 - E|3517 }E3402 - 3517
84X-RAY DIFFRACTION84{ F|3401 - F|3737 }F3401 - 3737
85X-RAY DIFFRACTION85{ E|3802 - E|3915 }E3802 - 3915
86X-RAY DIFFRACTION86{ F|3802 - F|4127 }F3802 - 4127
87X-RAY DIFFRACTION87{ E|4202 - E|4318 }E4202 - 4318
88X-RAY DIFFRACTION88{ F|4202 - F|4567 }F4202 - 4567
89X-RAY DIFFRACTION89{ E|4601 - E|4801 }E4601 - 4801
90X-RAY DIFFRACTION90{ F|4601 - F|4950 }F4601 - 4950
91X-RAY DIFFRACTION91{ E|5001 - E|5110 }E5001 - 5110
92X-RAY DIFFRACTION92{ F|5001 - F|5361 }F5001 - 5361
93X-RAY DIFFRACTION93{ E|5401 - E|5502 }E5401 - 5502
94X-RAY DIFFRACTION94{ F|5401 - F|5619 }F5401 - 5619
95X-RAY DIFFRACTION95{ E|5702 - E|5902 }E5702 - 5902
96X-RAY DIFFRACTION96{ F|5702 - F|5922 }F5702 - 5922
97X-RAY DIFFRACTION97{ E|6001 - E|6101 }E6001 - 6101
98X-RAY DIFFRACTION98{ F|6001 - F|6132 }F6001 - 6132
99X-RAY DIFFRACTION99{ E|6211 - E|6285 }E6211 - 6285
100X-RAY DIFFRACTION100{ F|6210 - F|6330 }F6210 - 6330
101X-RAY DIFFRACTION101{ E|6402 - E|6501 }E6402 - 6501
102X-RAY DIFFRACTION102{ F|6402 - F|6510 }F6402 - 6510
103X-RAY DIFFRACTION103{ E|6602 - E|6663 }E6602 - 6663
104X-RAY DIFFRACTION104{ F|6602 - F|6708 }F6602 - 6708
105X-RAY DIFFRACTION105{ G|2 - G|136 }G2 - 136

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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