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- PDB-4www: Crystal structure of the E. coli ribosome bound to CEM-101 -

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基本情報

登録情報
データベース: PDB / ID: 4www
タイトルCrystal structure of the E. coli ribosome bound to CEM-101
要素
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
キーワードRibosome/antibiotic / ribosomes / 70S / macrolide / ketolide / 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 / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / response to reactive oxygen species / ribosome assembly / transcription elongation factor complex / 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 / ribosome binding / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / 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 / cytoplasm / cytosol
類似検索 - 分子機能
Ribosomal protein L11, bacterial-type / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / 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, bacterial-type / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / 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 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 protein L17 signature. / 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 S3, bacterial-type / Ribosomal protein S19, 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 S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / 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 L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / 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 S16
類似検索 - ドメイン・相同性
Chem-EM1 / : / 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 ...Chem-EM1 / : / 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 str. K-12 substr. MG1655 (大腸菌)
Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.1 Å
データ登録者Dunkle, J.A. / Zhang, W. / Cate, J.H.D. / Mankin, A.S.
引用ジャーナル: Antimicrob. Agents Chemother. / 年: 2010
タイトル: Binding and action of CEM-101, a new fluoroketolide antibiotic that inhibits protein synthesis.
著者: Llano-Sotelo, B. / Dunkle, J. / Klepacki, D. / Zhang, W. / Fernandes, P. / Cate, J.H. / Mankin, A.S.
履歴
登録2014年11月12日登録サイト: RCSB / 処理サイト: RCSB
置き換え2014年12月24日ID: 4V80
改定 1.02014年12月24日Provider: repository / タイプ: Initial release
改定 1.12023年9月27日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
カテゴリ: atom_type / chem_comp ...atom_type / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_nat / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_nat.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _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 / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.d_res_high / _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
改定 1.22024年10月30日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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
RA: 23S rRNA
RB: 5S rRNA
RC: 50S ribosomal protein L2
RD: 50S ribosomal protein L3
RE: 50S ribosomal protein L4
RF: 50S ribosomal protein L5
RG: 50S ribosomal protein L6
RH: 50S ribosomal protein L9
RI: 50S ribosomal protein L11
RJ: 50S ribosomal protein L13
RK: 50S ribosomal protein L14
RL: 50S ribosomal protein L15
RM: 50S ribosomal protein L16
RN: 50S ribosomal protein L17
RO: 50S ribosomal protein L18
RP: 50S ribosomal protein L19
RQ: 50S ribosomal protein L20
RR: 50S ribosomal protein L21
RS: 50S ribosomal protein L22
RT: 50S ribosomal protein L23
RU: 50S ribosomal protein L24
RV: 50S ribosomal protein L25
RW: 50S ribosomal protein L27
RX: 50S ribosomal protein L28
RY: 50S ribosomal protein L29
RZ: 50S ribosomal protein L30
R0: 50S ribosomal protein L32
R1: 50S ribosomal protein L33
R2: 50S ribosomal protein L34
R3: 50S ribosomal protein L35
R4: 50S ribosomal protein L36
QA: 16S rRNA
QB: 30S ribosomal protein S2
QC: 30S ribosomal protein S3
QD: 30S ribosomal protein S4
QE: 30S ribosomal protein S5
QF: 30S ribosomal protein S6
QG: 30S ribosomal protein S7
QH: 30S ribosomal protein S8
QI: 30S ribosomal protein S9
QJ: 30S ribosomal protein S10
QK: 30S ribosomal protein S11
QL: 30S ribosomal protein S12
QM: 30S ribosomal protein S13
QN: 30S ribosomal protein S14
QO: 30S ribosomal protein S15
QP: 30S ribosomal protein S16
QQ: 30S ribosomal protein S17
QR: 30S ribosomal protein S18
QS: 30S ribosomal protein S19
QT: 30S ribosomal protein S20
QU: 30S ribosomal protein S21
XA: 16S rRNA
XB: 30S ribosomal protein S2
XC: 30S ribosomal protein S3
XD: 30S ribosomal protein S4
XE: 30S ribosomal protein S5
XF: 30S ribosomal protein S6
XG: 30S ribosomal protein S7
XH: 30S ribosomal protein S8
XI: 30S ribosomal protein S9
XJ: 30S ribosomal protein S10
XK: 30S ribosomal protein S11
XL: 30S ribosomal protein S12
XM: 30S ribosomal protein S13
XN: 30S ribosomal protein S14
XO: 30S ribosomal protein S15
XP: 30S ribosomal protein S16
XQ: 30S ribosomal protein S17
XR: 30S ribosomal protein S18
XS: 30S ribosomal protein S19
XT: 30S ribosomal protein S20
XU: 30S ribosomal protein S21
YA: 23S rRNA
YB: 5S rRNA
YC: 50S ribosomal protein L2
YD: 50S ribosomal protein L3
YE: 50S ribosomal protein L4
YF: 50S ribosomal protein L5
YG: 50S ribosomal protein L6
YH: 50S ribosomal protein L9
YI: 50S ribosomal protein L11
YJ: 50S ribosomal protein L13
YK: 50S ribosomal protein L14
YL: 50S ribosomal protein L15
YM: 50S ribosomal protein L16
YN: 50S ribosomal protein L17
YO: 50S ribosomal protein L18
YP: 50S ribosomal protein L19
YQ: 50S ribosomal protein L20
YR: 50S ribosomal protein L21
YS: 50S ribosomal protein L22
YT: 50S ribosomal protein L23
YU: 50S ribosomal protein L24
YV: 50S ribosomal protein L25
YW: 50S ribosomal protein L27
YX: 50S ribosomal protein L28
YY: 50S ribosomal protein L29
YZ: 50S ribosomal protein L30
Y0: 50S ribosomal protein L32
Y1: 50S ribosomal protein L33
Y2: 50S ribosomal protein L34
Y3: 50S ribosomal protein L35
Y4: 50S ribosomal protein L36
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)4,237,894468
ポリマ－4,228,144104
非ポリマー9,750364
水30,7701708
1
RA: 23S rRNA
RB: 5S rRNA
RC: 50S ribosomal protein L2
RD: 50S ribosomal protein L3
RE: 50S ribosomal protein L4
RF: 50S ribosomal protein L5
RG: 50S ribosomal protein L6
RH: 50S ribosomal protein L9
RI: 50S ribosomal protein L11
RJ: 50S ribosomal protein L13
RK: 50S ribosomal protein L14
RL: 50S ribosomal protein L15
RM: 50S ribosomal protein L16
RN: 50S ribosomal protein L17
RO: 50S ribosomal protein L18
RP: 50S ribosomal protein L19
RQ: 50S ribosomal protein L20
RR: 50S ribosomal protein L21
RS: 50S ribosomal protein L22
RT: 50S ribosomal protein L23
RU: 50S ribosomal protein L24
RV: 50S ribosomal protein L25
RW: 50S ribosomal protein L27
RX: 50S ribosomal protein L28
RY: 50S ribosomal protein L29
RZ: 50S ribosomal protein L30
R0: 50S ribosomal protein L32
R1: 50S ribosomal protein L33
R2: 50S ribosomal protein L34
R3: 50S ribosomal protein L35
R4: 50S ribosomal protein L36
QA: 16S rRNA
QB: 30S ribosomal protein S2
QC: 30S ribosomal protein S3
QD: 30S ribosomal protein S4
QE: 30S ribosomal protein S5
QF: 30S ribosomal protein S6
QG: 30S ribosomal protein S7
QH: 30S ribosomal protein S8
QI: 30S ribosomal protein S9
QJ: 30S ribosomal protein S10
QK: 30S ribosomal protein S11
QL: 30S ribosomal protein S12
QM: 30S ribosomal protein S13
QN: 30S ribosomal protein S14
QO: 30S ribosomal protein S15
QP: 30S ribosomal protein S16
QQ: 30S ribosomal protein S17
QR: 30S ribosomal protein S18
QS: 30S ribosomal protein S19
QT: 30S ribosomal protein S20
QU: 30S ribosomal protein S21
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,119,406236
ポリマ－2,114,07252
非ポリマー5,334184
水27015
タイプ名称対称操作数
identity operation1_555x,y,z1
2
XA: 16S rRNA
XB: 30S ribosomal protein S2
XC: 30S ribosomal protein S3
XD: 30S ribosomal protein S4
XE: 30S ribosomal protein S5
XF: 30S ribosomal protein S6
XG: 30S ribosomal protein S7
XH: 30S ribosomal protein S8
XI: 30S ribosomal protein S9
XJ: 30S ribosomal protein S10
XK: 30S ribosomal protein S11
XL: 30S ribosomal protein S12
XM: 30S ribosomal protein S13
XN: 30S ribosomal protein S14
XO: 30S ribosomal protein S15
XP: 30S ribosomal protein S16
XQ: 30S ribosomal protein S17
XR: 30S ribosomal protein S18
XS: 30S ribosomal protein S19
XT: 30S ribosomal protein S20
XU: 30S ribosomal protein S21
YA: 23S rRNA
YB: 5S rRNA
YC: 50S ribosomal protein L2
YD: 50S ribosomal protein L3
YE: 50S ribosomal protein L4
YF: 50S ribosomal protein L5
YG: 50S ribosomal protein L6
YH: 50S ribosomal protein L9
YI: 50S ribosomal protein L11
YJ: 50S ribosomal protein L13
YK: 50S ribosomal protein L14
YL: 50S ribosomal protein L15
YM: 50S ribosomal protein L16
YN: 50S ribosomal protein L17
YO: 50S ribosomal protein L18
YP: 50S ribosomal protein L19
YQ: 50S ribosomal protein L20
YR: 50S ribosomal protein L21
YS: 50S ribosomal protein L22
YT: 50S ribosomal protein L23
YU: 50S ribosomal protein L24
YV: 50S ribosomal protein L25
YW: 50S ribosomal protein L27
YX: 50S ribosomal protein L28
YY: 50S ribosomal protein L29
YZ: 50S ribosomal protein L30
Y0: 50S ribosomal protein L32
Y1: 50S ribosomal protein L33
Y2: 50S ribosomal protein L34
Y3: 50S ribosomal protein L35
Y4: 50S ribosomal protein L36
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,118,488232
ポリマ－2,114,07252
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)210.759, 433.272, 618.863
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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要素

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RNA鎖 , 3種, 6分子 RAYARBYBQAXA

#1: RNA鎖 23S rRNA


分子量: 941612.375 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Escherichia coli str. K-12 substr. MG1655 (大腸菌)
参照: GenBank: 545778205
#2: RNA鎖 5S rRNA


分子量: 38177.762 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Escherichia coli str. K-12 substr. MG1655 (大腸菌)
参照: GenBank: 545778205
#32: RNA鎖 16S rRNA


分子量: 496892.375 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Escherichia coli str. K-12 substr. MG1655 (大腸菌)
参照: GenBank: 545778205

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

#3: 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 (大腸菌) / 株: K12 / 参照: UniProt: P60422
#4: 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 (大腸菌) / 株: K12 / 参照: UniProt: P60438
#5: 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 (大腸菌) / 株: K12 / 参照: UniProt: P60723
#6: タンパク質 50S ribosomal protein L5


分子量: 20202.416 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: K12 / 参照: UniProt: P62399
#7: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0AG55
#8: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7R1
#9: タンパク質 50S ribosomal protein L11


分子量: 14763.165 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: K12 / 参照: UniProt: P0A7J7
#10: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0AA10
#11: タンパク質 50S ribosomal protein L14


分子量: 13451.910 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: K12 / 参照: UniProt: P0ADY3
#12: タンパク質 50S ribosomal protein L15


分子量: 14877.273 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: K12 / 参照: UniProt: P02413
#13: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0ADY7
#14: タンパク質 50S ribosomal protein L17


分子量: 13721.938 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: K12 / 参照: UniProt: P0AG44
#15: タンパク質 50S ribosomal protein L18


分子量: 12663.471 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: K12 / 参照: UniProt: P0C018
#16: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7K6
#17: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7L3
#18: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0AG48
#19: 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 (大腸菌) / 株: K12 / 参照: UniProt: P61175
#20: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0ADZ0
#21: 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 (大腸菌) / 株: K12 / 参照: UniProt: P60624
#22: 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 (大腸菌) / 株: K12 / 参照: UniProt: P68919
#23: タンパク質 50S ribosomal protein L27


分子量: 8476.680 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: K12 / 参照: UniProt: P0A7L8
#24: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7M2
#25: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7M6
#26: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0AG51
#27: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7N4
#28: タンパク質・ペプチド 50S ribosomal protein L33


分子量: 5814.842 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: K12 / 参照: UniProt: P0A7N9
#29: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7P5
#30: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7Q1
#31: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7Q6

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

#33: タンパク質 30S ribosomal protein S2


分子量: 24253.943 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: K12 / 参照: UniProt: P0A7V0
#34: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7V3
#35: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7V8
#36: タンパク質 30S ribosomal protein S5


分子量: 15804.282 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: K12 / 参照: UniProt: P0A7W1
#37: タンパク質 30S ribosomal protein S6


分子量: 11669.371 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: K12 / 参照: UniProt: P02358
#38: 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 (大腸菌) / 株: K12 / 参照: UniProt: P02359
#39: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7W7
#40: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7X3
#41: タンパク質 30S ribosomal protein S10


分子量: 11196.988 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: K12 / 参照: UniProt: P0A7R5
#42: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7R9
#43: タンパク質 30S ribosomal protein S12


分子量: 13636.961 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: K12 / 参照: UniProt: P0A7S3
#44: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7S9
#45: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0AG59
#46: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0ADZ4
#47: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7T3
#48: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0AG63
#49: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7T7
#50: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7U3
#51: タンパク質 30S ribosomal protein S20


分子量: 9506.190 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: K12 / 参照: UniProt: P0A7U7
#52: タンパク質 30S ribosomal protein S21


分子量: 6067.081 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: K12 / 参照: UniProt: P68679

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非ポリマー , 4種, 2072分子

#53: 化合物...
ChemComp-MG / MAGNESIUM ION


分子量: 24.305 Da / 分子数: 361 / 由来タイプ: 組換発現 / 式: Mg
#54: 化合物 ChemComp-EM1 / (3aS,4R,7S,9R,10R,11R,13R,15R,15aR)-1-{4-[4-(3-aminophenyl)-1H-1,2,3-triazol-1-yl]butyl}-4-ethyl-7-fluoro-11-methoxy-3a ,7,9,11,13,15-hexamethyl-2,6,8,14-tetraoxotetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-10-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside / CEM-101


分子量: 845.009 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C43H65FN6O10
#55: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 組換発現 / 式: Zn
#56: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1708 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY

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実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.37 Å3/Da / 溶媒含有率: 63.5 %
結晶化温度: 291 K / 手法: マイクロバッチ法 / pH: 6.5 / 詳細: PEG8k, MPD

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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: ALS / ビームライン: 12.3.1 / 波長: 1.1 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2009年6月13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: 1.1 Å / 相対比: 1
反射解像度: 3→69.783 Å / Num. obs: 1034420 / % possible obs: 97.76 % / 冗長度: 3.3 % / Biso Wilson estimate: 68.0827419216 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 8.27

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解析

ソフトウェア
名称分類
PHENIX精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3i1m, 3i1n, 3i1o, 3i1p

3i1m
PDB 未公開エントリ

3i1n
PDB 未公開エントリ

3i1o
PDB 未公開エントリ

3i1p
PDB 未公開エントリ


解像度: 3.1→69.7825450184 Å / SU ML: 0.420806247642 / 交差検証法: FREE R-VALUE / σ(F): 1.32616957969 / 位相誤差: 26.3782671321
Rfactor反射数%反射
Rfree0.25189911381 19579 2.01681105079 %
Rwork0.200038103937 951211 -
obs0.201089122939 970790 95.8379938181 %
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
原子変位パラメータBiso mean: 10.465297947 Å2
精密化ステップサイクル: LAST / 解像度: 3.1→69.7825450184 Å
タンパク質核酸リガンド溶媒全体
原子数89302 193031 423 1708 284464
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00574382867221306768
X-RAY DIFFRACTIONf_angle_d0.970596774181458740
X-RAY DIFFRACTIONf_chiral_restr0.071191118450458606
X-RAY DIFFRACTIONf_plane_restr0.0048912702576724677
X-RAY DIFFRACTIONf_dihedral_angle_d17.7088907215143049
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.13520.388497818935620.40787200283127240X-RAY DIFFRACTION83.14243847
3.1352-3.17210.3785310615065760.38851481624528043X-RAY DIFFRACTION85.3050761573
3.1721-3.21080.3791885779325980.37363428313828448X-RAY DIFFRACTION86.4901884882
3.2108-3.25140.3748897680725750.36346655995828904X-RAY DIFFRACTION87.714234706
3.2514-3.29420.3637776162415970.35316719453229367X-RAY DIFFRACTION89.3061516452
3.2942-3.33930.3248903742925610.29035973542429820X-RAY DIFFRACTION90.3497293761
3.3393-3.38710.3217621412846360.264081209730017X-RAY DIFFRACTION91.4278044561
3.3871-3.43760.3018933590226500.24366416661930524X-RAY DIFFRACTION92.7990950496
3.4376-3.49130.2834089196426600.23526232881330909X-RAY DIFFRACTION93.9329921447
3.4913-3.54860.3032886145696480.23507555615431372X-RAY DIFFRACTION95.1899637315
3.5486-3.60970.2883317278386360.22485088177731566X-RAY DIFFRACTION95.9192183963
3.6097-3.67540.2728591844946520.21219545041131859X-RAY DIFFRACTION96.6467493088
3.6754-3.74610.2571045331196380.20411241374432055X-RAY DIFFRACTION97.3150766483
3.7461-3.82250.2651830159926510.20045349490232355X-RAY DIFFRACTION97.9522792023
3.8225-3.90560.253553824076480.19486667912932457X-RAY DIFFRACTION98.3277889985
3.9056-3.99650.2404160225186800.17922841191332469X-RAY DIFFRACTION98.7018013994
3.9965-4.09640.2429073510346830.18307740491932648X-RAY DIFFRACTION98.9138498976
4.0964-4.20720.2371991668486510.18150361787132821X-RAY DIFFRACTION99.1234304667
4.2072-4.33090.2457380170197020.17334182937232771X-RAY DIFFRACTION99.302836122
4.3309-4.47070.2173484604686530.17080002576332917X-RAY DIFFRACTION99.5374488525
4.4707-4.63050.2236818855616980.16779125239232936X-RAY DIFFRACTION99.7390427614
4.6305-4.81580.2113395596667210.16021696053333014X-RAY DIFFRACTION99.7545685729
4.8158-5.03490.218183219676830.16640541081233058X-RAY DIFFRACTION99.7310238827
5.0349-5.30030.2347521955656670.16599104112433077X-RAY DIFFRACTION99.7281002483
5.3003-5.63230.2230884659166730.15962891869733099X-RAY DIFFRACTION99.728325065
5.6323-6.06690.2285157056527110.16588832271433166X-RAY DIFFRACTION99.8320268757
6.0669-6.6770.2539976873846960.1755827825633220X-RAY DIFFRACTION99.8234047563
6.677-7.64210.2167527438596930.16224768758833440X-RAY DIFFRACTION99.9034127495
7.6421-9.62430.2343410939456710.17758233960233624X-RAY DIFFRACTION99.9242446316
9.6243-69.80020.213250860627090.18310580757734015X-RAY DIFFRACTION98.9231382827
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)
10.06710.0092-0.07590.1464-0.03340.13960.02040.07440.0088-0.2139-0.072-0.1201-0.0912-0.1178-0.0160.39420.17790.20280.29610.20420.3366-62.093312.6296-76.2395
20.002-0.00360.00080.0133-0.00730.00460.00730.01570.0092-0.0044-0.01-0.0112-0.01230.0048-00.44210.14290.03090.32450.06550.4524-85.463636.2955-31.0982
30.0029-0.0032-0.00060.00330.00060.0001-0.0030.00040.0057-0.0091-0.0003-0.0034-0.0089-000.56110.11490.01630.50990.08640.5903-98.1656.9954-40.0107
40.0015-0.0011-0.00050.0017-0.00070.001-0.007-0.0005-0.0063-0.0016-0.0005-0.00190.00040.0002-00.5720.06140.01740.54450.10510.579-79.525455.3562-47.3636
50.00170.00010.00050.00710.00170.00090.0024-0.00320.00520.00240.0021-0.0034-0.007-0.0019-00.9060.0282-0.00220.74310.03260.9549-86.12485.639-19.9606
60.0001-0.00010.00010.0004-0.00010.00010.0005-0.00230.0022-0.0009-0.00150.0010.0022-0.0022-01.00420.023-0.00420.9942-0.00051.0099-117.895684.3027-17.6605
70.1456-0.051-0.01690.0549-0.04330.09570.05910.00120.02220.04750.13420.01770.0687-0.1221-0.00010.47750.170.16860.35250.22350.5202-145.893944.045-3.5416
80.00320.00290.00070.0032-0.00020.00240.00720.0018-0.00730.003-0.0058-0.00040.0006-0.00401.1537-0.0172-0.03671.1390.04671.1403-167.910220.3944-45.6058
90.1368-0.11190.04520.1259-0.01720.1005-0.0567-0.06970.25240.11330.0672-0.1256-0.13-0.0257-0.00490.38920.0708-0.05180.0969-0.00420.4705-64.295938.6871-2.7709
100.00790.018500.1055-0.06590.0564-0.0619-0.00070.0088-0.0425-0.0704-0.0451-0.00440.001-0.01280.23990.08570.17970.23280.12140.3626-55.5751-6.5957-42.0266
110.0987-0.0005-0.0650.08020.00220.184-0.072-0.0582-0.18180.1260.00760.0140.0550.089700.6736-0.0238-0.17790.21070.05080.4408-29.10934.7737103.8561
120.00680.00830.00880.00930.01030.0114-0.00120.0199-0.0179-0.0252-0.0182-0.0119-0.0142-0.0368-00.5002-0.184-0.22210.33910.0170.2879-40.841781.716575.1959
130.0005-00.00080.00010.00020.00090.00090.01010.0027-0.00160.00160.00430.00020.004-00.5328-0.0617-0.11050.4744-0.02590.4726-51.089873.622552.6808
140.00050.00040.00050.00070.00010.0006-0.004-0.00540.0014-0.0008-0.003-0.00380.00640.0145-00.6073-0.089-0.07630.5169-0.03450.5766-34.335463.599358.17
150.00250.0013-0.00160.001-0.00060.0040.0060.01280.0021-0.0103-0.00020.0009-0.0013-0.002100.9685-0.0472-0.00740.9394-0.03510.8395-30.748989.727926.2235
160.00030.000300.000500.00060.00090.00270.00220.00070.00060.0017-0.001-0.0023-01.20670.0004-0.00631.20440.00131.1939-61.739196.618721.4939
170.0827-0.03620.01690.02280.02050.0633-0.1010.02140.0740.14220.08660.0530.03760.0032-00.5643-0.1501-0.23850.36170.15580.536-95.0402114.65454.8972
180.0021-0.0008-0.00090.0016-0.00140.00180.00470.0067-0.00860.0006-0.00980.01470.0013-0.0116-01.7737-0.029-0.00371.78640.0231.7868-125.334375.303573.871
190.17670.1130.05860.21750.01090.0405-0.01530.0265-0.01730.0475-0.0628-0.1575-0.09790.0761-0.30770.532-0.2765-0.16020.20840.05010.1355-14.8711106.250975.8744
200.02440.03130.01030.05690.03880.0343-0.0898-0.005-0.0695-0.00620.0466-0.04720.05130.0914-00.7449-0.0463-0.1980.61720.10670.53-22.697569.3242123.433
210.1199-0.0303-0.0140.1410.02920.0687-0.0077-0.01190.03080.14680.0214-0.0404-0.03720.0040.0234-0.2426-0.0468-0.10640.0609-0.022-0.0076-64.9421-59.49715.1176
220.02570.00450.01440.0079-0.00490.010.0711-0.04890.0073-0.03940.0373-0.0315-0.065-0.0129-00.36460.0088-0.11220.4210.1020.5432-139.0256-50.4103-62.9902
230.0024-0.0005-0.00010-0.00010.0002-0.008-0.00910.0061-0.00890.00880.00740.0021-0.00400.4834-0.02670.01020.52680.0150.465-102.8242-3.9093-3.3971
240.00340.00320.00210.00750.00540.00340.003-0.0022-0.01220.00180.04390.0128-0.0303-0.057400.43590.01360.0280.4092-0.05280.4503-94.719619.20478.8397
250.0005-0.0002-0.00030.0005-0.00030.0006-0.00240.00940.0113-0.0012-0.00490.002-0.0048-0.0006-01.29210.00150.01271.26510.00051.291-148.0079-27.1024-12.1618
260.0089-0.00060.00720.0109-0.0020.0072-0.00220.04010.0051-0.00420.0173-0.0013-0.06990.0548-00.2298-0.00780.00520.43940.04250.4778-165.2315-23.314616.2986
270.0267-0.0122-0.00290.00810.00270.00830.0234-0.0007-0.01410.0094-0.08460.0422-0.00540.0029-00.05650.0170.14130.3533-0.02450.4805-173.6743-53.665730.2975
280.0124-0.00140.00410.0496-0.01980.0186-0.04620.00450.0198-0.0303-0.02760.04990.0004-0.0326-0.0002-0.005-0.0065-0.02190.2727-0.08670.2826-142.8533-79.9947-7.8139
290.00080.0006-0.00130.0009-0.00140.00250.0028-0.00430.01120.0029-0.00030.006-0.0121-0.0066-01.0256-0.0114-0.00521.0128-0.02151.0014-64.515220.5256121.9515
300.0606-0.0181-0.1320.1341-0.05120.3821-0.0661-0.29060.00110.24040.21710.1184-0.16360.2590.02110.6793-0.2359-0.16350.5286-0.2445-0.0531-30.0803131.1724170.6302
310.00930.00490.00130.00280.00130.00250.0256-0.00670.0166-0.00670.00890.00740.00390.004301.9527-0.02060.02142.0075-0.01941.9738-116.654172.0317149.8837
320.00080.0004-0.00140.0002-0.00070.0023-0.00450.00030.00150.0002-0.00580.0014-0.00470.0076-00.9194-0.10920.02650.883-0.03810.8954-60.2278115.5976109.6762
330.0046-0.0037-0.00030.0035-0.00210.0025-0.01860.00440.0219-0.0147-0.01610.0355-0.0096-0.022-0.00011.26040.01320.05441.27190.00871.2792-28.5965193.195190.5045
340.000700.00050.00040.00050.0009-0.0013-00.0016-0.0004-0.0013-0.0009-0-0.0008-01.9527-0.0009-0.00661.9607-0.0111.9593-110.1482124.8681131.9044
350.00330.00090.00010.00220.00140.0028-0.00980.00120.0034-0.0108-0.0079-0.00450.00280.0024-0.00011.38340.00160.00191.414-0.00831.4011-121.2353152.2611115.834
360.0113-0.0073-0.00180.0053-0.00040.0018-0.004-0.0104-0.0140.00080.00150.0180.0074-0.010601.23870.12640.02721.28970.08791.3159-129.2086170.5556143.0612
370.0040.0014-0.00360.0014-0.00240.0062-0.01940.0229-0.00260.0008-0.0090.00710.0157-0.021200.93160.07810.06181.06290.10440.9736-113.6375128.4329176.3239
380.0013-0.00060.00050.00230.00040.00040.00220.01070.0059-0.0068-0.00330.0026-0.0046-0.007900.93410.01030.01250.90940.0120.916111.3204227.249388.4593
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1((chain QA and (resid 2:8 or resid 27:557)) or (chain QD and resid 1:205) or (chain QP and resid 1:82) or (chain QT and resid 2:86) or (chain QL and resid 22:123) or (chain ZQ and (resid 299 or resid 315 or resid 362 or resid 417 or resid 509 or resid 547 or resid 533 or resid 608 or resid 536 or resid 116 or resid 352 or resid 324 or resid 100 or resid 195 or resid 259 or resid 258)))Q0
2X-RAY DIFFRACTION2((chain QA and (resid 9:26 or resid 558:562 or resid 564:566 or resid 914:925 or resid 1391:1396)) or (chain QL and resid 1:21) or (chain ZQ and (resid 21 or resid 560)))Q0
3X-RAY DIFFRACTION3(chain QE and resid 9:73)Q0
4X-RAY DIFFRACTION4(chain QE and resid 74:149)Q0
5X-RAY DIFFRACTION5(chain QB and (resid 8:107 or resid 147:225))Q0
6X-RAY DIFFRACTION6(chain QB and resid 108:146)Q0
7X-RAY DIFFRACTION7((chain QA and (resid 926:986 or resid 1048:1390)) or (chain QC and resid 1:206) or (chain QG and resid 1:151) or (chain QI and resid 3:129) or (chain QJ and resid 5:102) or (chain QM and resid 1:114) or (chain QN and resid 1:100) or (chain QS and resid 2:80) or (chain ZQ and (resid 934 or resid 937 or resid 980 or resid 1048 or resid 1076 or resid 1054 or resid 1303 or resid 1386 or resid 964 or resid 1222 or resid 1110 or resid 1108)))Q0
8X-RAY DIFFRACTION8(chain QA and resid 987:1047)Q0
9X-RAY DIFFRACTION9((chain QA and (resid 563 or resid 567:913 or resid 1496:1530)) or (chain QF and resid 1:100) or (chain QH and resid 1:129) or (chain QK and resid 12:128) or (chain QO and resid 1:88) or (chain QR and resid 19:73) or (chain QU and resid 3:53) or (chain ZQ and (resid 572 or resid 578 or resid 593 or resid 770 or resid 814 or resid 891 or resid 1500 or resid 1499 or resid 781 or resid 869 or resid 1525)))Q0
10X-RAY DIFFRACTION10((chain QA and resid 1397:1495) or (chain ZQ and (resid 1417 or resid 8201)))Q0
11X-RAY DIFFRACTION11((chain XA and (resid 2:8 or resid 27:557)) or (chain XD and resid 1:205) or (chain XP and resid 1:82) or (chain XT and resid 2:86) or (chain XL and resid 22:123) or (chain ZU and (resid 299 or resid 315 or resid 362 or resid 417 or resid 509 or resid 547 or resid 533 or resid 608 or resid 536 or resid 116 or resid 352 or resid 324 or resid 100 or resid 195 or resid 259 or resid 258)))X0
12X-RAY DIFFRACTION12((chain XA and (resid 9:26 or resid 558:562 or resid 564:566 or resid 914:925 or resid 1391:1396)) or (chain XL and resid 1:21) or (chain ZU and (resid 21 or resid 560)))X0
13X-RAY DIFFRACTION13(chain XE and resid 9:73)X0
14X-RAY DIFFRACTION14(chain XE and resid 74:149)X0
15X-RAY DIFFRACTION15(chain XB and (resid 8:107 or resid 147:225))X0
16X-RAY DIFFRACTION16(chain XB and resid 108:146)X0
17X-RAY DIFFRACTION17((chain XA and (resid 926:986 or resid 1048:1390)) or (chain XC and resid 1:206) or (chain XG and resid 1:151) or (chain XI and resid 3:129) or (chain XJ and resid 5:102) or (chain XM and resid 1:114) or (chain XN and resid 1:100) or (chain XS and resid 2:80) or (chain ZU and (resid 934 or resid 937 or resid 980 or resid 1048 or resid 1076 or resid 1054 or resid 1303 or resid 1386 or resid 964 or resid 1222 or resid 1110 or resid 1108)))X0
18X-RAY DIFFRACTION18(chain XA and resid 987:1047)X0
19X-RAY DIFFRACTION19((chain XA and (resid 563 or resid 567:913 or resid 1496:1530)) or (chain XF and resid 1:100) or (chain XH and resid 1:129) or (chain XK and resid 12:128) or (chain XO and resid 1:88) or (chain XR and resid 19:73) or (chain XU and resid 3:53) or (chain ZU and (resid 572 or resid 578 or resid 593 or resid 770 or resid 814 or resid 891 or resid 1500 or resid 1499 or resid 781 or resid 869 or resid 1525)))X0
20X-RAY DIFFRACTION20((chain XA and resid 1397:1495) or (chain ZU and (resid 1417 or resid 8201)))X0
21X-RAY DIFFRACTION21((chain RA 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 RC and resid 1:271) or (chain RS and resid 1:110) or (chain RT and resid 1:93) or (chain RU and resid 1:102) or (chain RD and resid 1:209) or (chain RE and resid 1:201) or (chain RG and resid 1:176) or (chain RJ and resid 1:142) or (chain RK and resid 1:122) or (chain RL and resid 2:144) or (chain RM and resid 1:136) or (chain RN and resid 1:120) or (chainRR0
22X-RAY DIFFRACTION22((chain RA and resid 1039:1115) or (chain RI and resid 1:141))R0
23X-RAY DIFFRACTION23(chain RA and resid 1906:1929)R0
24X-RAY DIFFRACTION24(chain RA and resid 2093:2197)R0
25X-RAY DIFFRACTION25(chain RA and resid 877:901)R0
26X-RAY DIFFRACTION26((chain RA and resid 2297:2321) or (chain RF and resid 1:177) or (chain ZR and resid 2304))R0
27X-RAY DIFFRACTION27((chain RB and (resid 2:69 or resid 108:119)) or (chain RO and resid 2:117))R0
28X-RAY DIFFRACTION28((chain RB and resid 70:107) or (chain RV and resid 1:94) or (chain ZR and resid 6095:6100))R0
29X-RAY DIFFRACTION29(chain RH and resid 49:149)R0
30X-RAY DIFFRACTION30((chain YA 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 YC and resid 1:271) or (chain YS and resid 1:110) or (chain YT and resid 1:93) or (chain YU and resid 1:102) or (chain YD and resid 1:209) or (chain YE and resid 1:201) or (chain YG and resid 1:176) or (chain YJ and resid 1:142) or (chain YK and resid 1:122) or (chain YL and resid 2:144) or (chain YM and resid 1:136) or (chain YN and resid 1:120) or (chainYY0
31X-RAY DIFFRACTION31((chain YA and resid 1039:1115) or (chain YI and resid 1:141))Y0
32X-RAY DIFFRACTION32(chain YA and resid 1906:1929)Y0
33X-RAY DIFFRACTION33(chain YA and resid 2093:2197)Y0
34X-RAY DIFFRACTION34(chain YA and resid 877:901)Y0
35X-RAY DIFFRACTION35((chain YA and resid 2297:2321) or (chain YF and resid 1:177) or (chain ZT and resid 2304))Y0
36X-RAY DIFFRACTION36((chain YB and (resid 2:69 or resid 108:119)) or (chain YO and resid 2:117))Y0
37X-RAY DIFFRACTION37((chain YB and resid 70:107) or (chain YV and resid 1:94) or (chain ZT and resid 6095:6100))Y0
38X-RAY DIFFRACTION38(chain YH and resid 49:149)Y0

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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