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- PDB-4ybb: High-resolution structure of the Escherichia coli ribosome -

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基本情報

登録情報
データベース: PDB / ID: 4ybb
タイトルHigh-resolution structure of the Escherichia coli ribosome
要素
  • (23S rRNA) x 2
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 31
  • 16S rRNA
  • 5S rRNA
キーワードRIBOSOME / Protein biosynthesis / ribosomes / RNA / transfer / exit / peptidyl / 30S / 70S / 16S / ribosomal subunit / posttranscriptional modification / posttranslational modification
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 / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / 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 / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / translational termination / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / regulation of mRNA stability / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / ribosome assembly / transcription elongation factor complex / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / response to reactive oxygen species / DNA endonuclease activity / transcription antitermination / regulation of cell growth / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / ribosome biogenesis / large ribosomal subunit / regulation of translation / transferase activity / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small 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 S21 superfamily ...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 S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / 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 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 S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-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 S9, bacterial/plastid / 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 L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily
類似検索 - ドメイン・相同性
ACETIC ACID / GUANINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 1,4-DIAMINOBUTANE / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) ...ACETIC ACID / GUANINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 1,4-DIAMINOBUTANE / SPERMIDINE / : / 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 K-12 (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: 2.1 Å
データ登録者Noeske, J. / Wasserman, M.R. / Terry, D.S. / Altman, R.B. / Blanchard, S.C. / Cate, J.H.D.
引用ジャーナル: Nat.Struct.Mol.Biol. / 年: 2015
タイトル: High-resolution structure of the Escherichia coli ribosome.
著者: Noeske, J. / Wasserman, M.R. / Terry, D.S. / Altman, R.B. / Blanchard, S.C. / Cate, J.H.
履歴
登録2015年2月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02015年3月18日Provider: repository / タイプ: Initial release
改定 1.12015年4月15日Group: Database references
改定 2.02023年9月27日Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity_poly / entity_src_nat / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _chem_comp.mon_nstd_flag / _database_2.pdbx_DOI ..._chem_comp.mon_nstd_flag / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_alt_source_flag / _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 / _pdbx_struct_oper_list.symmetry_operation / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 2.12023年11月15日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / struct_conn / struct_ref
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.pdbx_seq_one_letter_code
改定 2.22025年2月12日Group: Data collection / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order
改定 2.32025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
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
CA: 23S rRNA
CB: 5S rRNA
CC: 50S ribosomal protein L2
CD: 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
C0: 50S ribosomal protein L30
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
DA: 23S rRNA
DB: 5S rRNA
DC: 50S ribosomal protein L2
DD: 50S ribosomal protein L3
DE: 50S ribosomal protein L4
DF: 50S ribosomal protein L5
DG: 50S ribosomal protein L6
DH: 50S ribosomal protein L9
DI: 50S ribosomal protein L10
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
D0: 50S ribosomal protein L30
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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)4,270,475651
ポリマ－4,249,827105
非ポリマー20,649546
水139,6167750
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
DA: 23S rRNA
DB: 5S rRNA
DC: 50S ribosomal protein L2
DD: 50S ribosomal protein L3
DE: 50S ribosomal protein L4
DF: 50S ribosomal protein L5
DG: 50S ribosomal protein L6
DH: 50S ribosomal protein L9
DI: 50S ribosomal protein L10
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
D0: 50S ribosomal protein L30
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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,147,580397
ポリマ－2,132,05353
非ポリマー15,528344
水84747
タイプ名称対称操作数
identity operation1_555x,y,z1
2
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
CA: 23S rRNA
CB: 5S rRNA
CC: 50S ribosomal protein L2
CD: 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
C0: 50S ribosomal protein L30
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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,122,895254
ポリマ－2,117,77452
非ポリマー5,121202
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)212.170, 433.890, 624.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain AC and resid 2004:2227 and not (resid 2165 or resid 2188 or resid 2204:2205)
21chain AF and resid 2004:2227 and not (resid 2165 or resid 2188 or resid 2204:2205)

NCSドメイン領域:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYILEILEchain AC and resid 2004:2227 and not (resid 2165 or resid 2188 or resid 2204:2205)ACC2 - 2071 - 206
2METMETLYSLYSchain AF and resid 2004:2227 and not (resid 2165 or resid 2188 or resid 2204:2205)AFF1 - 1061 - 106

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要素

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RNA鎖 , 4種, 6分子 AABACACBDBDA

#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 K-12 (大腸菌) / 参照: GenBank: 731469900
#22: 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 K-12 (大腸菌) / 参照: GenBank: 731469900
#23: 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 K-12 (大腸菌) / 参照: GenBank: 731469900
#53: RNA鎖 23S rRNA


分子量: 941505.375 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: GenBank: 731469900

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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 ... , 31種, 59分子 CCDCCDCEDECFDFCGDGCHDHCJDJCKDKCLDLCMDMCNDNCODOCPDPCQDQCRDRCS...

#24: 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
#25: タンパク質 50S ribosomal protein L3


分子量: 22277.535 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: P60438
#26: 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
#27: 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
#28: 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
#29: 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
#30: 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
#31: 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
#32: 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
#33: 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
#34: 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
#35: 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
#36: 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
#37: 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
#38: 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
#39: 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
#40: 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
#41: 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
#42: 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
#43: 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
#44: 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
#45: 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
#46: 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
#47: 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
#48: 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
#49: 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 (大腸菌) / 株: K12 / 参照: UniProt: P0A7N9
#50: 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
#51: 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
#52: 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
#54: タンパク質 50S ribosomal protein L3


分子量: 22291.562 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: UniProt: P60438
#55: 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 , 14種, 8296分子

#56: 化合物...
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 463 / 由来タイプ: 合成 / 式: Mg
#57: 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
#58: 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
#59: 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
#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-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
#63: 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
#64: 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
#65: 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
#66: 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
#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: 7750 / 由来タイプ: 天然 / 式: H2O

-
詳細

Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 32

-
試料調製

結晶マシュー密度: 3.39 Å3/Da / 溶媒含有率: 63.68 %
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: 8.3.1 / 波長: 1.1 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2013年2月1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: 2→69.388 Å / Num. obs: 3309372 / % possible obs: 86.9 % / Observed criterion σ(I): -3 / 冗長度: 3.97 % / Biso Wilson estimate: 52.53 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.154 / Rrim(I) all: 0.169 / Χ2: 1.019 / Net I/σ(I): 4.77 / Num. measured all: 13135436
反射 シェル

Diffraction-ID: 1 / Rejects: _

解像度 (Å)最高解像度 (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.050.0253.3860.162042662809131079024.10538.4
2.05-2.110.0722.3570.213306512737821670232.84261
2.11-2.170.1371.6880.284493522663102153202.05280.9
2.17-2.240.2081.3220.374955912586392206111.60485.3
2.24-2.310.3121.0410.495236352507872200401.25687.7
2.31-2.390.4310.8420.655698622426032186471.01190.1
2.39-2.480.5550.6640.885911852340862137060.79291.3
2.48-2.580.6980.5021.226096802255052089340.59492.7
2.58-2.70.80.3851.766331172162182038530.45394.3
2.7-2.830.8690.32.526360442068651957740.35194.6
2.83-2.980.9110.263.776793751967591891430.396.1
2.98-3.160.8890.3435.768575371862821841950.38698.9
3.16-3.380.9270.3327.779811611751721739640.36599.3
3.38-3.650.9580.2549.379965451631841621900.27899.4
3.65-40.9750.1911.249869731503221493310.20699.3
4-4.470.9830.15813.059671691361261353440.1799.4
4.47-5.160.9890.12915.229246811203721197350.13899.5
5.16-6.320.9930.10616.877954181019301013720.11399.5
6.32-8.940.9950.08318.660890279323788360.08999.4
8.940.9990.04622.0129429244449434520.0597.8

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解析

ソフトウェア
名称バージョン分類
PHENIX精密化
XSCALEデータスケーリング
PDB_EXTRACT3.15データ抽出
XDSデータ削減
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4V9D

4v9d


解像度: 2.1→69.388 Å / SU ML: 0.36 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 33.45 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2338 10048 0.33 %
Rwork0.2185 3053878 -
obs0.2186 3063926 93.05 %
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 max: 177.73 Å2 / Biso mean: 88.4994 Å2 / Biso min: 42.42 Å2
精密化ステップサイクル: final / 解像度: 2.1→69.388 Å
タンパク質核酸リガンド溶媒全体
原子数18770 32930 131 549 52380
Biso mean--70.82 63.63 -
残基数----3916
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.008313573
X-RAY DIFFRACTIONf_angle_d1.27469224
X-RAY DIFFRACTIONf_chiral_restr0.05259448
X-RAY DIFFRACTIONf_plane_restr0.00725195
X-RAY DIFFRACTIONf_dihedral_angle_d15.521145369
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11AC2627X-RAY DIFFRACTION3.562TORSIONAL
12AF2627X-RAY DIFFRACTION3.562TORSIONAL
LS精密化 シェル

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

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.12390.42481590.4089857668592579
2.1239-2.14890.3921810.3883880728825381
2.1489-2.17510.37511890.3727902909047983
2.1751-2.20260.35632000.353919899218984
2.2026-2.23160.35092230.3445943619458486
2.2316-2.26220.34332280.3269946989492687
2.2622-2.29450.34412360.3151958539608988
2.2945-2.32870.33962640.3249974759773989
2.3287-2.36510.32612810.3177983309861190
2.3651-2.40390.2832870.3112987219900891
2.4039-2.44530.3143030.3039995549985791
2.4453-2.48980.31343120.292710004810036092
2.4898-2.53770.33123210.275510051810083992
2.5377-2.58950.28323360.273910211810245494
2.5895-2.64580.29383460.272710278910313594
2.6458-2.70740.27863460.26410302310336994
2.7074-2.77510.28633480.27210318710353594
2.7751-2.85010.27673560.266310379810415495
2.8501-2.9340.26113730.253510482410519796
2.934-3.02870.26453900.241410664710703798
3.0287-3.13690.26224290.229510833710876699
3.1369-3.26250.23594340.210810858710902199
3.2625-3.4110.24274360.205810863610907299
3.411-3.59080.22584360.199210884410928099
3.5908-3.81580.23154360.190310887110930799
3.8158-4.11040.20124360.187510897910941599
4.1104-4.52390.21674380.186510928110971999
4.5239-5.17840.19884390.180710954710998699
5.1784-6.52340.18844410.181710987011031199
6.5234-69.42620.21194440.190511086511130999
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)
10.8875-0.1967-0.19340.76930.01530.51710.11760.40010.1867-0.5101-0.1504-0.2254-0.1709-0.00280.02280.79960.07280.1350.51980.2640.5651-61.687612.9358-75.0567
20.10510.1207-0.00890.1531-0.05750.27690.02640.04920.0621-0.0353-0.0322-0.0067-0.11010.04910.00230.63430.0977-0.00110.4150.17010.7137-86.30636.2636-31.1071
31.79160.8986-1.14220.9599-0.73371.21870.10250.32230.433-0.04730.15380.3649-0.3214-0.274-0.25730.80060.1798-0.02840.64880.20030.9199-98.813656.8689-40.0979
40.6620.4525-0.04320.41620.07090.1017-0.04620.19030.2247-0.09640.0089-0.02-0.23440.09670.03450.99060.08350.02030.68140.31410.9629-78.460557.2218-47.4594
50.5168-0.0460.19850.09730.00950.4007-0.04960.04560.3167-0.02590.05580.0739-0.232-0.0051-0.00581.30350.0717-0.06760.66290.16741.4131-85.823985.8409-19.1954
60.3813-0.3227-0.18630.70840.30790.49780.07870.06980.20270.012-0.07740.2327-0.2866-0.3203-0.01111.23290.12630.01621.06950.10421.3135-115.501583.1626-19.6386
70.72320.1362-0.07480.1309-0.1110.53420.087-0.08710.19510.06660.10310.2234-0.1627-0.2923-0.18450.80450.19590.14620.62540.27121.0546-146.069343.0555-3.0331
80.6773-0.18640.19240.1680.12950.33930.01380.15340.0523-0.1772-0.03370.1345-0.1513-0.22960.02211.5026-0.0851-0.03771.41370.10441.6791-168.561521.3022-46.4537
90.4022-0.04830.04370.5145-0.19570.67790.0096-0.07720.32220.18530.0068-0.1514-0.41490.0884-0.01790.65640.0239-0.04530.30270.00880.7476-64.859738.6747-2.7233
100.31870.0457-0.09750.4953-0.05070.3988-0.06720.16740.0516-0.0869-0.056-0.24050.05590.0790.10150.49960.00390.04210.39470.18730.5806-56.2295-6.7-41.9101
110.3377-0.0103-0.07060.2504-0.00990.1789-0.0092-0.0740.07020.08270.0071-0.0467-0.03250.0440.00290.21130.0106-0.03510.1620.00410.1787-65.9601-59.919614.8416
120.9265-0.2958-0.00031.1615-0.04761.0317-0.00650.38771.0048-0.58450.01420.0788-0.8199-0.3558-0.01751.07610.0408-0.14661.22640.37881.5813-143.6183-55.8883-66.113
130.9255-0.06450.83020.29580.09511.5547-0.0459-0.0455-0.0968-0.18850.14490.17940.1647-0.3678-0.0970.6175-0.07470.03840.66220.05460.704-103.4159-3.9216-3.3395
140.54480.1407-0.17760.4526-0.26820.60060.1462-0.33510.24090.44270.11390.432-0.2784-0.639-0.21471.4006-0.02280.27831.41-0.10111.5549-100.745721.229990.7375
150.13980.1644-0.00592.0271-0.73950.2952-0.02520.11960.24290.1057-0.0234-0.008-0.2467-0.03450.04321.5527-0.05040.09871.2442-0.02921.4667-149.2194-26.8805-11.7974
160.6963-0.36480.21961.34440.24551.1391-0.09320.30730.3919-0.07990.0188-0.1089-0.37220.33450.05570.4121-0.0625-0.0020.62510.18730.8238-166.4055-23.682516.3769
170.5318-0.38220.10220.66720.17090.4999-0.00070.0349-0.08510.0912-0.07350.37550.0497-0.18730.06040.3440.01770.13860.48340.05020.7119-174.6341-53.904130.4645
180.2443-0.1980.27840.6570.42781.2376-0.0141-0.0270.06950.03150.00930.1692-0.0182-0.1321-0.00090.212-0.01230.040.24140.01990.3628-138.5004-72.871711.7228
190.27310.49250.20630.88410.37160.15770.0493-0.034-0.02910.055-0.08810.1370.1391-0.17660.03691.5819-0.199-0.01951.4884-0.05731.3876-61.154517.0377119.077
200.8339-0.01120.26720.17530.17950.7205-0.0272-0.2041-0.35190.23990.0661-0.13860.22930.2053-0.02131.151-0.0087-0.16180.50040.10320.8328-28.046235.7763104.1689
210.24690.111-0.0930.43080.02840.1525-0.0488-0.0761-0.06360.054-0.0011-0.1711-0.01940.01070.04631.1047-0.2601-0.26730.5060.07450.5027-41.391581.87576.173
221.3089-1.0248-0.48161.17850.45730.53170.05660.1931-0.1663-0.1893-0.16670.1390.0742-0.11270.10311.2576-0.2607-0.2990.7966-0.03450.7547-51.415973.836253.8362
230.35-0.112-0.140.16190.06990.292-0.01170.1307-0.2015-0.0754-0.0225-0.02120.13820.01780.03091.219-0.1612-0.19450.8307-0.04931.0212-32.771163.419257.5334
240.32760.07550.05380.1071-0.02110.1209-0.00980.239-0.0516-0.1795-0.0289-0.01210.0739-0.02950.03181.6773-0.1537-0.04421.3857-0.10391.035-30.098190.43827.1248
251.5267-0.92460.66230.5629-0.38520.80650.34390.0799-0.1242-0.2244-0.1620.32230.1734-0.1657-0.17991.3577-0.0626-0.10961.236-0.0361.2183-59.572294.516524.2918
261.3142-0.07250.07890.41430.07290.6262-0.1105-0.00770.61460.03130.04690.5241-0.2719-0.42980.05341.201-0.0661-0.19191.0010.13961.3874-95.0461115.353156.7805
270.26220.0013-0.10950.1399-0.02830.16420.057-0.0372-0.04460.0271-0.07570.12620.0595-0.11950.01592.1243-0.15780.0312.25910.03242.0429-125.091372.881173.5058
280.79440.15950.02030.89430.16520.3610.12760.00280.0340.087-0.1336-0.3661-0.16890.10650.0131.0225-0.2298-0.18860.55730.10740.5121-15.2401106.470776.9645
290.15050.0919-0.12360.32230.18560.2938-0.247-0.1432-0.11980.16460.2354-0.02650.00890.09530.01151.147-0.0676-0.14780.81620.10780.6992-23.143869.1836124.6559
300.3432-0.0521-0.22940.2998-0.03460.56850.041-0.32510.12820.20410.0787-0.0466-0.25530.3744-0.09711.1886-0.2671-0.11411.0157-0.12590.5338-30.4517130.627172.2518
310.3698-0.0052-0.09830.3294-0.07580.26930.18570.11820.0603-0.2032-0.0228-0.0380.1440.0859-0.13192.0003-0.0233-0.01392.2699-0.07012.1604-116.908271.6057151.8157
321.07940.4887-0.17570.9707-0.32290.33340.046-0.0585-0.20960.1273-0.10630.28990.258-0.25110.05671.2202-0.29270.09491.1195-0.07261.05-60.5957115.4319111.0396
330.38010.0271-0.07910.07010.08410.34090.0024-0.09460.31230.16870.02140.3221-0.3562-0.4708-0.02541.65150.08840.19711.7401-0.01741.6142-32.939202.913988.6869
340.0049-0.0075-0.02480.03160.09910.33870.02430.0636-0.0158-0.07480.0427-0.0115-0.0320.0237-0.05621.82170.01020.02581.88840.03161.8084-110.6795119.8022125.321
350.01680.02350.02160.0395-0.0020.12670.02560.1525-0.0774-0.11730.018-0.00310.0375-0.0366-0.03452.03480.0389-0.02982.1007-0.07071.9846-121.3153152.2408117.7066
360.1012-0.05270.07190.3434-0.1340.1122-0.02340.13220.1413-0.06830.11330.2831-0.1526-0.2465-0.07891.6970.32450.03921.76320.24951.8726-129.5549170.6541145.0175
370.25770.1558-0.16590.1508-0.020.23930.03150.07250.1005-0.04050.03890.1195-0.1696-0.1922-0.05921.32690.1480.10521.31020.18271.2342-103.1822145.3846171.3391
380.52730.0129-0.46050.0318-0.00740.7101-0.0496-0.1286-0.00290.1005-0.01750.0880.1111-0.18720.06281.356-0.10180.25531.02470.04861.353414.9951224.863795.0493
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
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70X-RAY DIFFRACTION33(chain AG and resid 5093:5197) or (chain AH and resid 9518:9724)AH9518 - 9724
71X-RAY DIFFRACTION34chain AG and resid 3877:3901AG3877 - 3901
72X-RAY DIFFRACTION35(chain AG and resid 5297:5321) or (chain AH and resid 901:1077)AG5297 - 5321
73X-RAY DIFFRACTION35(chain AG and resid 5297:5321) or (chain AH and resid 901:1077)AH901 - 1077
74X-RAY DIFFRACTION36(chain AG and (resid 6002:6069 or resid 6108:6119)) or (chain AH and resid 3002:3117)AG6002 - 6069
75X-RAY DIFFRACTION36(chain AG and (resid 6002:6069 or resid 6108:6119)) or (chain AH and resid 3002:3117)AG6108 - 6119
76X-RAY DIFFRACTION37(chain AG and resid 6070:6107) or (chain AH and resid 5008:5083)AG6070 - 6107
77X-RAY DIFFRACTION37(chain AG and resid 6070:6107) or (chain AH and resid 5008:5083)AH5008 - 5083
78X-RAY DIFFRACTION38chain AH and resid 8048:8148AH8048 - 8148

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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