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- PDB-4dr6: Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal... -

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基本情報

登録情報
データベース: PDB / ID: 4dr6
タイトルCrystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position and streptomycin bound
要素
  • (30S ribosomal protein ...) x 20
  • 16S rRNA
  • 5'-R(*UP*UP*U)-3'
  • 5'-R(*UP*UP*UP*U)-3'
  • 5'-R(P*CP*UP*UP*GP*AP*GP*GP*(PSU)P*GP*GP*U)-3'
  • 5'-R(P*UP*UP*GP*AP*GP*GP*(PSU)P*GP*G)-3'
キーワードRIBOSOME/ANTIBIOTIC / decoding / Streptomycin / RNA structure / antibiotic resistance / RIBOSOME-ANTIBIOTIC complex
機能・相同性
機能・相同性情報


ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
類似検索 - 分子機能
S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain ...S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / Ribosomal Protein S8; Chain: A, domain 1 - #30 / Ribosomal protein S3 C-terminal domain / Ribosomal protein S6/Translation elongation factor EF1B / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / S15/NS1, RNA-binding / Helix hairpin bin / Ribosomal Protein S7 / Ribosomal protein S7/S5 / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / K homology (KH) domain / Helicase, Ruva Protein; domain 3 - #50 / Double Stranded RNA Binding Domain - #20 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / GMP Synthetase; Chain A, domain 3 / Ribosomal Protein S5; domain 2 / Ribosomal protein S14, type Z / Double Stranded RNA Binding Domain / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Few Secondary Structures / Irregular / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / : / Ribosomal protein S5, N-terminal, conserved site
類似検索 - ドメイン・相同性
STREPTOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 ...STREPTOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / 30S ribosomal protein S17 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
類似検索 - 構成要素
生物種Thermus thermophilus (バクテリア)
手法X線回折 / シンクロトロン / フーリエ合成 / 解像度: 3.3 Å
データ登録者Demirci, H. / Murphy IV, F. / Murphy, E. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
引用ジャーナル: Nat Commun / 年: 2013
タイトル: A structural basis for streptomycin-induced misreading of the genetic code.
著者: Demirci, H. / Murphy, F. / Murphy, E. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
履歴
登録2012年2月16日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02012年11月14日Provider: repository / タイプ: Initial release
改定 1.12013年1月23日Group: Database references
改定 1.22013年1月30日Group: Database references
改定 1.32025年2月19日Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: 16S rRNA
B: 30S ribosomal protein S2
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
U: 30S ribosomal protein THX
V: 5'-R(*UP*UP*UP*U)-3'
W: 5'-R(P*UP*UP*GP*AP*GP*GP*(PSU)P*GP*G)-3'
a: 5'-R(P*CP*UP*UP*GP*AP*GP*GP*(PSU)P*GP*GP*U)-3'
b: 5'-R(*UP*UP*U)-3'
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)802,309404
ポリマ－792,45825
非ポリマー9,851379
水16,340907
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)402.600, 402.600, 174.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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要素

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RNA鎖 , 5種, 5分子 AVWab

#1: RNA鎖 16S rRNA


分子量: 494170.781 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: GenBank: M26923.1
#22: RNA鎖 5'-R(*UP*UP*UP*U)-3'


分子量: 1179.706 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: mRNA A Site / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8
#23: RNA鎖 5'-R(P*UP*UP*GP*AP*GP*GP*(PSU)P*GP*G)-3'


分子量: 2928.774 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: ASL (Leucine 2) A Site / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8
#24: RNA鎖 5'-R(P*CP*UP*UP*GP*AP*GP*GP*(PSU)P*GP*GP*U)-3'


分子量: 3540.122 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: ASL (Leucine 2) Shine Dalgarno mini helix / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8
#25: RNA鎖 5'-R(*UP*UP*U)-3'


分子量: 873.540 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: mRNA / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8

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30S ribosomal protein ... , 20種, 20分子 BCDEFGHIJKLMNOPQRSTU

#2: タンパク質 30S ribosomal protein S2


分子量: 29317.703 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: P80371
#3: タンパク質 30S ribosomal protein S3


分子量: 26751.076 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: P80372
#4: タンパク質 30S ribosomal protein S4


分子量: 24373.447 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: P80373
#5: タンパク質 30S ribosomal protein S5


分子量: 17583.416 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: Q5SHQ5
#6: タンパク質 30S ribosomal protein S6


分子量: 11988.753 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: Q5SLP8
#7: タンパク質 30S ribosomal protein S7


分子量: 18050.973 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: P17291
#8: タンパク質 30S ribosomal protein S8


分子量: 15868.570 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS
#9: タンパク質 30S ribosomal protein S9


分子量: 14410.614 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: P80374
#10: タンパク質 30S ribosomal protein S10


分子量: 11954.968 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: Q5SHN7
#11: タンパク質 30S ribosomal protein S11


分子量: 13737.868 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: P80376
#12: タンパク質 30S ribosomal protein S12


分子量: 14966.846 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: F6DEQ7, UniProt: Q5SHN3*PLUS
#13: タンパク質 30S ribosomal protein S13


分子量: 14338.861 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: P80377
#14: タンパク質 30S ribosomal protein S14


分子量: 7158.725 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS
#15: タンパク質 30S ribosomal protein S15


分子量: 10578.407 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: Q5SJ76
#16: タンパク質 30S ribosomal protein S16


分子量: 10409.983 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: Q5SJH3
#17: タンパク質 30S ribosomal protein S17


分子量: 12324.670 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS
#18: タンパク質 30S ribosomal protein S18


分子量: 10258.299 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: Q5SLQ0
#19: タンパク質 30S ribosomal protein S19


分子量: 10605.464 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: Q5SHP2
#20: タンパク質 30S ribosomal protein S20


分子量: 11736.143 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: P80380
#21: タンパク質・ペプチド 30S ribosomal protein THX


分子量: 3350.030 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: Q5SIH3

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非ポリマー , 4種, 1286分子

#26: 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: 376 / 由来タイプ: 合成 / 式: Mg
#27: 化合物 ChemComp-SRY / STREPTOMYCIN / STREPTOMYCIN A / ストレプトマイシン


分子量: 581.574 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C21H39N7O12 / コメント: 薬剤, 抗生剤*YM
#28: 化合物 ChemComp-ZN / ZINC ION


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


分子量: 18.015 Da / 分子数: 907 / 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

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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: 4.47 Å3/Da / 溶媒含有率: 72.49 %
結晶化温度: 277 K / 手法: ハンギングドロップ法 / pH: 6.5 / 詳細: MPD, pH 6.5, HANGING DROP, temperature 277K

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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: NSLS / ビームライン: X25 / 波長: 1.1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2011年6月28日
放射モノクロメーター: double crystal Si(111) monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification
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
Reflection数: 2412927 / Rmerge(I) obs: 0.092 / D res high: 3.3 Å / Num. obs: 213602 / % possible obs: 99.9
Diffraction reflection shell
最高解像度 (Å)最低解像度 (Å)Num. obs% possible obs (%)IDRmerge(I) obs
14.7650256796.510.03
10.4414.76458210010.035
8.5210.44584710010.039
7.388.52682910010.044
6.67.38769410010.049
6.026.6846610010.058
5.586.02920910010.063
5.225.58983610010.07
4.925.221046910010.078
4.674.921102010010.091
4.454.671159710010.105
4.264.451208810010.133
4.094.261262310010.167
3.944.091309010010.221
3.813.941355210010.285
3.693.811399210010.376
3.583.691441310010.526
3.483.581486110010.729
3.393.481524710010.939
3.33.391562010011.174
反射解像度: 3.3→50 Å / Num. all: 213602 / Num. obs: 213602 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 104.363 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 18.75
反射 シェル
解像度 (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
3.3-3.390.0122.02178392156201100
3.39-3.480.0122.62176841152471100
3.48-3.580.0123.36165923148611100
3.58-3.690.0124.68169268144131100
3.69-3.810.0126.49162400139921100
3.81-3.940.0128.41150652135521100
3.94-4.090.01210.84152802130901100
4.09-4.260.01213.95145282126231100
4.26-4.450.01217.34136093120881100
4.45-4.670.01221.73134360115971100
4.67-4.920.01224.54122061110201100
4.92-5.220.01228.82119686104691100
5.22-5.580.01231.5610925598361100
5.58-6.020.01234.8110441692091100
6.02-6.60.01236.529379184661100
6.6-7.380.01242.128513476941100
7.38-8.520.01246.247273968291100
8.52-10.440.01249.936161858471100
10.44-14.760.01254.054728945821100
14.76-500.01254.5249252567196.5

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解析

ソフトウェア
名称バージョン分類NB
XSCALEデータスケーリング
PHENIXdev_978精密化
PDB_EXTRACT3.1データ抽出
HKL-2000データ収集
XDSデータ削減
PHENIXdev_978位相決定
精密化構造決定の手法: フーリエ合成 / 解像度: 3.3→49.484 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8899 / SU ML: 0.33 / σ(F): 1.99 / 位相誤差: 17.93 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.1918 10749 5.03 %FROM PDB ENTRY 2VQE
Rwork0.1534 ---
obs0.1554 213574 99.97 %-
all-213574 --
溶媒の処理減衰半径: 0.86 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 57.15 Å2 / ksol: 0.262 e/Å3
原子変位パラメータBiso max: 550 Å2 / Biso mean: 120.8243 Å2 / Biso min: 26.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.4527 Å20 Å20 Å2
2--2.4527 Å20 Å2
3---10.6777 Å2
精密化ステップサイクル: LAST / 解像度: 3.3→49.484 Å
タンパク質核酸リガンド溶媒全体
原子数19127 33097 418 907 53549
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00657427
X-RAY DIFFRACTIONf_angle_d0.94685762
X-RAY DIFFRACTIONf_chiral_restr0.06510541
X-RAY DIFFRACTIONf_plane_restr0.0054924
X-RAY DIFFRACTIONf_dihedral_angle_d17.61626342
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.3-3.33740.31353420.258666186960
3.3374-3.37670.26073840.239367177101
3.3767-3.41780.28473520.228966707022
3.4178-3.46110.2483390.215967127051
3.4611-3.50660.24593660.21266977063
3.5066-3.55470.25373520.208766987050
3.5547-3.60540.25053610.203466677028
3.6054-3.65920.25423830.186767097092
3.6592-3.71640.21083500.171967007050
3.7164-3.77730.19893610.163667047065
3.7773-3.84240.19443840.157666787062
3.8424-3.91220.19473560.15767097065
3.9122-3.98750.18753400.151967647104
3.9875-4.06880.19173440.147867317075
4.0688-4.15720.20893450.143667277072
4.1572-4.25390.18513590.1467357094
4.2539-4.36020.18433510.136267187069
4.3602-4.4780.17443700.131367707140
4.478-4.60970.18283160.128367777093
4.6097-4.75840.17263520.127867277079
4.7584-4.92830.17383320.120167937125
4.9283-5.12540.15933410.123267857126
5.1254-5.35840.17123820.132267497131
5.3584-5.64060.16863420.125468127154
5.6406-5.99340.1623900.122367857175
5.9934-6.45520.18143440.127768397183
6.4552-7.10320.1643470.124968647211
7.1032-8.12710.15693700.126468667236
8.1271-10.22440.18693990.154169337332
10.2244-49.48920.21683950.206271717566
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)
10.43770.136-0.16050.5838-0.11270.5273-0.003-0.032-0.05050.16320.08680.17250.1630.0792-0.07820.5770.1530.06340.5768-0.03260.817143.70683.4459-12.1861
21.9945-0.31570.2790.4806-0.08860.3594-0.0296-0.99510.46190.29030.0973-0.1681-0.15580.0818-0.06840.8338-0.16690.04981.6391-0.60861.1678222.8545129.25899.8616
31.70670.698-0.63720.41-0.510.2852-0.2608-0.1499-0.6323-0.25540.1627-0.5140.27970.19960.09070.92260.18380.05120.9094-0.09651.0837163.470169.0326-25.1122
42.76441.29491.39332.9191-2.26084.37080.391-0.07183.12410.5747-0.5708-1.0079-1.1022-0.17320.08581.828-0.24590.22961.4785-0.04751.7125181.227132.097-40.4929
55.63960.37462.49374.5804-4.04526.047-0.37890.42661.14740.02990.3719-0.3101-0.96060.2613-0.01792.0253-0.10710.53470.7363-0.04681.2722157.3934156.9003-35.9141
64.11940.61143.4496.00481.97675.66160.1868-0.00871.228-0.8061-0.34790.7739-0.8712-1.02340.13631.30010.06210.39960.82550.0771.8603150.8497155.9118-27.1545
76.32120.3767-0.32215.2711-2.30296.62530.26160.66041.4239-0.7493-0.1864-0.6346-1.39611.7577-0.07991.105-0.33430.59291.1694-0.08451.5776167.4805162.1616-18.7011
83.32992.11960.46513.9921-2.29624.11180.5119-0.75411.09730.3862-0.0534-0.2525-0.79380.9169-0.41630.7522-0.28480.44561.0559-0.58661.5295174.5213156.8813-6.4097
94.47681.1020.61155.8707-0.92081.6146-0.12960.45421.03841.47441.061-1.5796-0.51522.0192-0.84461.6212-0.4660.02232.0787-0.77522.2374190.7094161.5066-3.9051
102.9047-0.47021.84184.89-0.94893.4610.05510.16040.2043-0.77770.3052-0.3971-0.69880.391-0.33121.1844-0.12080.62780.7632-0.25671.6557160.6985156.0966-18.1448
111.32721.61460.59967.1634-1.93091.637-0.1685-0.05340.18990.40850.01570.3048-0.3845-0.0640.13342.3328-0.20440.32030.6306-0.00442.505163.9368174.221-22.928
120.1152-0.28720.16120.8597-0.39140.2328-0.0133-0.8180.25110.57280.15910.1843-0.3462-0.2673-0.03571.330.01290.06972.7507-1.00721.268205.2787140.988534.2517
131.0912-1.8749-0.16443.24980.22611.671-0.1514-1.30620.1830.43090.20490.63020.1481-0.73120.04960.9256-0.09680.21092.633-0.74711.2992190.3185132.506418.3293
147.1832-7.1602-3.00627.25423.13024.04230.2413-1.01110.32520.62140.50130.1709-0.81370.4925-0.74831.667-0.31530.13131.2557-0.17541.1184153.9536111.284838.067
156.48880.08631.12953.6925-0.77082.53350.1083-1.35110.86590.7503-0.1333-0.3991-0.72070.7640.04651.1179-0.04920.0940.9856-0.25660.7152160.3059112.974225.7591
162.3731.09291.15963.0572-3.6227.33860.3186-0.18470.23960.6082-0.15430.25510.313-0.1719-0.15411.20540.14420.38450.6611-0.09770.94136.0301103.939431.2148
174.1413-1.89811.6163.350.85794.04480.2632-1.80170.57171.92620.16770.5248-0.7111-0.4418-0.39892.14780.02160.49771.331-0.23711.0067132.3233110.344647.6953
186.48790.4893-5.68575.1509-0.36514.97441.39410.03551.7780.1429-0.0442-0.0119-1.679-0.1593-1.3560.89660.11040.12230.57430.0390.841139.6965114.149323.52
196.0282-6.236-6.00796.44646.17856.4704-0.6498-1.79281.36611.47890.43870.0651-0.15760.16830.1270.8977-0.02530.07451.5486-0.62261.3179162.1133126.428.5214
204.8661-1.7638-4.93084.16772.0765.021-0.1691-0.28820.13940.4454-0.10350.0014-0.1250.29780.24440.8102-0.19250.14771.8302-0.56741.041184.1399121.568-2.0195
214.8080.3073-2.88824.9676-1.56346.23730.3729-0.5031.30410.55950.6786-0.3239-0.05040.6613-0.99650.739-0.2370.19680.9721-0.55191.0573162.0523129.09985.0333
227.0075-5.0955.45156.8046-2.56796.2987-0.6218-0.21492.05471.09680.6699-0.7714-1.25891.06980.01551.074-0.27850.16730.9026-0.50031.6018167.9398132.98935.7353
237.82866.066-2.78828.1917-2.1811.87470.6547-1.00062.65021.0978-0.38441.4528-0.4466-0.6184-0.2870.63940.02340.18770.876-0.2671.1929145.4855129.10120.8883
243.01131.3693-2.97318.3681-0.46323.0386-0.54782.967-1.6361-0.6437-0.18451.5651.401-1.9660.67580.5692-0.0950.021.1482-0.21011.0847152.7424119.8695-10.3996
257.54992.896-4.58584.9418-3.74577.7022-0.10190.07870.31450.39070.2338-0.0146-0.0522-0.6512-0.12950.50750.07520.14730.5319-0.26991.0713145.6554116.56731.3301
262.02710.65692.12472.03150.95254.0024-0.1694-0.63740.30040.3480.10160.33770.060.7530.04990.559-0.06980.21310.7326-0.24190.7979153.3903120.4586-0.0427
279.7806-5.50445.58213.098-3.14273.1907-0.4278-0.78761.46010.4148-0.07660.4948-1.3979-1.45850.46660.89960.1850.27330.9029-0.22541.3176136.6359133.6256-8.9581
282.32250.3639-3.47323.91760.93715.7565-0.03371.6679-0.0612-1.38350.10250.17530.1793-0.1183-0.0451.15180.1328-0.09482.33530.01590.665174.1655114.784-93.1846
298.60262.07412.54834.70620.09244.81380.08621.7104-0.1551-0.92820.0314-0.2842-0.31690.072-0.1190.98960.15510.20891.36150.04810.7442175.0837115.6123-86.8059
306.87745.55325.08714.58294.15133.7808-1.01610.30432.4282-1.4701-0.08332.031-1.7999-0.45011.05211.36540.2650.04571.34280.4551.7977165.7581131.4971-73.5266
313.70222.77821.86082.23941.08531.5746-0.1352-0.43192.98540.3186-0.3131.1598-1.33990.4090.40181.1172-0.29430.06971.3203-0.64722.3011217.6421143.0997-22.6294
326.53346.09790.1086.26210.30950.2219-0.3210.63590.6281-0.5270.1132-0.2081-0.09210.11320.18461.3613-0.16220.53461.08790.38473.1509239.2366153.1206-24.4864
338.77042.8842-3.01465.5542-2.94518.7749-0.23070.50971.12150.1040.009-0.6523-0.6711.41940.19960.7417-0.14820.20411.0882-0.14211.7862245.0379143.7627-22.5039
347.9273.6561-2.52996.7446-0.88443.01780.1178-0.08461.05230.1441-0.14960.5519-0.3394-0.14210.01921.4248-0.82780.46841.7907-0.18582.7077253.4786147.6885-36.5125
359.16497.68545.52579.52884.13276.7095-0.54461.00320.2354-0.45310.1134-0.0081-0.36-0.31660.35350.96060.28030.29641.60720.15831.1741233.2176137.4235-37.1623
366.32645.930.57795.69850.57045.55660.1485-0.3411-0.337-0.28750.74731.22230.9426-0.208-0.83871.09510.1563-0.19792.04190.45871.5965219.5769125.5777-38.6411
371.5603-1.6821-1.47413.69080.88321.66160.0290.01381.01420.00050.0504-0.283-0.38030.0077-0.08440.7712-0.31980.17071.1877-0.06811.6761235.0239136.4296-30.5134
384.3753-3.19994.8095.494-2.02156.15760.18811.0920.9935-0.73520.0647-1.0955-0.022.0785-0.20320.7552-0.13290.4661.3826-0.15481.5174250.5843135.2934-30.2891
396.9245-0.20553.7043.25632.21913.6581-0.48691.9678-0.3801-0.93650.3161-0.89960.28510.63850.12721.2658-0.15720.15911.85850.04231.4598237.7046129.4278-40.1899
409.29691.14876.56652.14120.43164.71450.3822-0.00061.49740.7898-0.34431.7959-1.1579-1.5786-0.05761.39530.63710.42371.8624-0.01631.8946219.3847125.8877-44.6485
416.87321.0127-0.18947.7444-0.44221.71150.52610.00660.57540.03290.25930.1396-0.14610.4729-0.74490.47020.16090.25370.6553-0.060.8269140.1512122.7088-30.3506
429.3928.52377.60927.76586.92926.18270.127-0.12511.3405-0.2367-0.13830.5564-0.6882-0.25760.05220.65960.16960.27180.718-0.03121.075139.3723132.308-31.4762
432.70822.75512.56576.9625.50755.46040.0497-0.27920.7053-0.1937-0.58461.672-0.9419-2.21280.53980.48790.18930.15240.79690.1971.3226126.6872125.8637-27.324
443.7253-1.434-1.7553.71913.61163.54960.03750.29380.45520.05220.18741.0532-1.3966-0.887-0.22341.00020.10660.15890.7310.22231.53130.6184133.0958-29.7149
455.64471.43625.13253.66552.65646.0695-0.03310.29641.0115-0.80520.21910.1663-1.12770.2257-0.21020.80490.08060.17950.55130.14071.2505133.5959131.8698-38.4318
469.53460.76675.31144.2706-0.58027.38040.15-0.43251.13520.74280.6410.1703-0.4435-0.1112-0.75960.79140.02630.31520.6687-0.06271.3135145.7397140.0393-16.7243
477.85337.02876.2016.39785.93876.28350.44490.08280.05190.3749-0.1142-0.6689-0.00120.1397-0.30340.48290.10780.19360.49480.10121.0915143.4364129.3158-18.4462
481.29352.2552-1.06924.4349-3.52039.9158-0.21990.0175-0.0370.03730.0842-0.40440.85410.71120.09040.58250.1190.09170.55040.03181.088133.8873108.8729-24.2379
498.1476-3.87777.25512.5345-2.4267.9928-0.5666-0.6806-2.12880.93190.67160.45522.10321.2384-0.09960.93290.35370.42710.80260.18531.6877125.5825109.7467-12.0318
502.7274.38451.60427.48761.98942.02530.9486-0.7769-0.11281.1052-0.7287-0.55461.258-1.5472-0.19920.8215-0.15140.04941.31520.10161.0967134.1892119.3597-8.6969
516.97235.46926.67457.45556.83188.11330.09560.19550.04340.33940.0939-0.0351-0.0008-0.1034-0.20430.64240.26110.26330.71760.05851.0645126.3187118.872-18.8087
527.57083.1216-1.16584.6918-3.51272.87980.0544-0.76381.61320.475-0.057-0.2123-1.0488-0.3126-0.02340.75530.15920.3140.7160.02531.7081122.5005119.9066-15.4552
532.7172.0746-1.58329.01742.63334.38090.23880.0147-0.6860.04840.1637-0.00170.27560.3502-0.40770.55380.15350.16440.42390.12790.8912131.2681117.2473-18.8115
541.281.05181.00679.39452.07012.13730.1707-0.14071.02140.0345-0.12170.4996-0.87370.3546-0.00271.3081-0.38060.16611.4645-0.90593.0068238.9768167.1648-3.7997
558.32023.48546.18692.52253.00545.32690.09580.0996-0.5480.2479-0.0518-1.1126-0.35630.9754-0.06461.3129-0.4943-0.24541.7878-0.83782.7715249.2774162.4376-3.1801
562.56593.0238-0.14053.99230.41872.7612-0.31640.15340.7074-0.1397-0.3995-0.1-0.76651.06630.66771.1215-0.63220.10651.7438-0.4362.5743244.4611159.2299-12.7041
571.8869-1.30720.91682.8004-0.0182.49970.26430.28950.75510.6454-0.0811-0.1802-0.92980.7335-0.15161.4212-0.4560.1611.2013-0.55793.1942239.1973165.1951-7.5923
580.4036-1.3351-1.40786.8877.81359.04380.1639-0.65312.2220.34870.09350.3275-1.65710.5816-0.24661.9763-0.0368-0.01850.9822-0.32142.5826229.1709172.7722-15.8952
591.0884-0.67460.4674.6279-1.93093.38810.192-0.68681.25140.4966-0.2793-0.5419-0.84960.38120.07921.0981-0.36380.20041.4513-0.58651.8549225.8613147.6491-5.7234
606.2436-3.71862.67372.4481-2.79137.61840.4676-0.0993-0.4594-1.0984-0.19210.87761.5043-0.783-0.2471.0719-0.33570.06781.7815-0.84251.227222.6523124.7233-6.8484
613.24211.59872.68360.79261.3722.55070.4333-0.46110.71160.9942-0.76030.4405-0.6461-0.23510.37991.6075-0.2359-0.11032.39-1.38282.7354221.2991162.153527.859
621.6106-3.4725-2.88077.97295.57545.97270.1061-0.49271.20651.17630.14-0.377-2.40420.2134-0.28972.5562-0.0263-0.11632.1678-1.48422.7055227.2583165.957123.686
635.78471.20083.88592.16780.96727.36230.2928-0.88870.46541.5508-0.3694-0.8284-0.5290.57390.04171.3708-0.26520.12222.4305-0.93911.4388225.2745142.07617.9352
642.8730.51371.0941.0258-0.84041.5711-0.2805-0.6090.96190.2510.2356-0.0881-0.36610.28820.03871.0914-0.24860.20622.0959-0.80521.2901218.3892135.306913.6759
652.6307-0.67211.11558.1286-1.14551.17370.4496-1.36130.86212.4352-1.0420.9848-1.1049-0.61140.6622.2816-0.2151-0.29582.4599-1.59833.1331230.0343169.436531.7503
664.5694-5.7227-3.12987.37642.84997.58980.039-0.89251.34980.3940.16040.7624-1.46510.3907-0.23972.49630.28980.63752.338-1.14422.2997222.8514171.146240.391
675.8546-5.2475-4.98684.83924.55514.30130.4931-0.90471.18461.40370.2717-2.0655-1.53172.9408-0.78331.6421-0.3090.1763.0468-0.77272.3026215.5683157.760336.2131
687.4138-5.1566-1.18944.4674-2.02429.42220.6947-0.34930.52161.4611-0.2165-1.4672-0.74391.8947-0.52561.96050.0713-0.52062.8116-1.16161.8335227.4678156.256634.062
698.7672-1.93986.21299.7972-2.84425.1782-0.49520.5312-0.0967-0.30180.4786-0.3531-0.3017-0.25220.04290.4627-0.01090.17230.7699-0.11670.8886213.158118.5943-69.2536
707.0803-0.50121.69874.4442-0.60356.5885-0.08060.11960.3055-0.166-0.0364-0.8156-0.01391.86460.11790.6968-0.12270.22421.1738-0.01740.925217.3025114.8981-62.5371
714.13433.6267-5.06746.6818-4.23886.21820.0647-0.05990.4261-0.2029-0.0375-1.1642-0.19561.57-0.04740.5583-0.02890.09771.1677-0.10591.0113221.2417121.9611-64.3926
724.67861.61695.50822.0790.46787.8849-0.4038-0.6370.540.0908-0.45940.3531-0.2762-0.62290.80190.71920.00770.23340.9266-0.17361.0843211.3838125.8974-64.7432
733.0675-0.62512.90278.61995.23886.7477-0.21050.67271.2068-0.696-0.5582-1.2027-1.05911.29470.76260.8985-0.14470.17730.94370.29331.1029211.0102129.728-69.7464
740.94780.25520.83846.2851-4.48334.33330.23810.51530.05290.279-0.0455-0.0772-0.28230.4179-0.21081.0379-0.0560.45571.2932-0.33361.19193.7347110.2081-57.5097
752.6332-1.63163.75351.0002-2.32515.32840.3836-0.0651-0.2535-0.15430.36470.08060.74110.4429-0.72350.69540.316-0.04791.02060.13451.2097153.299189.0035-13.2323
764.40920.4821-2.30033.93991.14731.7781-0.1899-0.0983-0.38810.40720.2668-0.65140.56360.8844-0.05680.68610.3042-0.18621.01910.04730.9378173.876579.03510.8826
775.0471-3.55652.1913.0755-0.32614.3827-0.1391-0.1453-2.0029-0.46870.05360.92420.76370.67780.00280.8852-0.07380.22931.7577-0.48362.4096274.0032116.6762-8.1766
784.4448-6.21343.97748.6958-5.42795.2279-0.00470.34840.8674-0.13190.32431.0413-0.061-0.1355-0.30510.64030.3114-0.191.5782-0.36161.7655268.8301120.9716-5.159
796.74143.8725-0.25924.4577-3.1414.2038-0.0416-0.46510.63450.1097-0.8865-0.8308-0.10330.92260.91240.7102-0.00190.09421.9227-0.50531.9243275.9917122.7674-0.9486
808.7637.6596-2.35329.2325-2.65282.17440.5067-1.9933-0.57961.1615-0.8911-1.4084-0.48571.13220.3840.9269-0.0638-0.16231.8345-0.06131.0821265.5499105.08918.9516
812.6228-3.12431.1079.1743-3.77114.9456-0.0546-0.994-0.29560.7296-0.2478-0.3540.20540.51760.26590.9416-0.04530.04632.4293-0.2461.2341249.984999.278313.906
824.11743.44853.59764.06541.17686.0987-0.3132-0.1019-1.06440.04630.40870.33820.13540.9969-0.08920.69730.08820.04221.5432-0.15841.275240.988103.81912.4567
838.1201-2.4107-2.20634.3693-3.89557.22230.4196-0.98240.13110.8958-0.4241-0.2079-0.0688-0.56080.00521.0171-0.4938-0.07072.8148-0.60351.3709220.5487117.239834.3622
843.45190.0061-2.0595.01094.73075.7327-0.7551-3.1422.13932.09881.8917-0.76960.05652.0375-1.13061.3562-0.14980.03012.821-0.68781.9898232.1104118.889139.7495
850.26150.985-0.10393.7787-0.26720.27520.309-0.9323-0.02330.3783-0.0986-0.0125-0.31260.3436-0.22051.0027-0.20410.13662.5448-0.52971.4048228.4715121.226730.7577
861.63633.41322.96217.11796.17835.36220.1611-0.1203-0.00081.0650.2048-0.98260.92621.1161-0.38610.98510.1539-0.34252.3539-0.50751.1169215.7497124.65427.0206
872.2269-0.0372-0.74812.1068-0.70823.9812-0.0863-1.05610.98580.3263-0.36610.16180.3878-0.12680.37770.95330.1211-0.04412.2609-0.86621.2914216.7172134.312320.522
885.65255.2816-4.48444.9384-4.18043.604-0.58794.37121.7576-2.47430.68360.5692-0.5751-0.6439-0.13511.16590.1515-0.04941.79470.35591.0007141.4082110.7414-73.9276
897.6647-4.8858-0.63053.18650.82228.33610.45821.2144-0.5511-0.6545-0.01150.5406-0.5031-0.2568-0.39920.6560.0698-0.1490.7555-0.01131.0218145.0101104.3475-66.3479
909.4051-1.85321.18423.0816-0.29231.71230.2687-1.3592-0.14060.19750.2345-0.01490.18810.6738-0.49870.61820.0093-0.12921.1725-0.11790.7236143.7808101.902-56.2219
915.0463-0.0192-4.39575.57570.54623.87940.00291.3291-2.2223-0.0861-0.07871.03731.0528-1.28460.0910.8013-0.1499-0.31291.39370.19191.8417131.333297.7799-63.6279
928.1444-0.26643.55950.8768-0.87053.01560.0239-0.7240.27430.3680.35610.2512-0.1716-0.1293-0.35871.03520.10970.52730.69510.03281.3152117.490676.974715.4409
932.321-0.40040.53670.3874-1.17565.1293-0.1291-0.23690.87140.39410.2810.71160.0135-0.0385-0.16620.83360.04220.30050.6015-0.02951.5828115.042477.321610.9058
945.30074.32925.58283.57934.38766.5644-0.7547-0.60292.2533-0.4833-0.23820.8198-2.6976-0.75430.99781.36180.20460.53470.6746-0.01841.7399109.707786.511320.9646
955.47810.8464-0.37961.7145-3.68868.9219-0.0632-0.15390.5508-0.3947-0.073-0.1225-0.6855-0.13860.10811.01520.3010.33580.73270.36772.0417100.99279.39595.8698
966.34283.66655.45095.75412.18318.91320.3116-1.0263-0.07530.6808-0.11640.9039-0.1957-0.7858-0.20151.1797-0.0640.79150.69610.16671.8502101.245175.145716.7365
972.1880.72281.25022.91833.01313.2451-0.19090.94360.4156-0.73240.2258-0.41710.02310.0335-0.02940.8153-0.01730.19830.91370.28380.7754120.284280.8273-38.1483
981.58550.2776-0.1462.98490.43972.9968-0.15830.09180.2074-0.5880.24690.74110.1318-0.3886-0.07370.6723-0.0937-0.10180.78610.20981.2075122.216184.6572-35.269
994.5206-4.0555-0.04454.1049-1.62025.9283-0.3802-0.05850.4832-0.19640.3836-0.41510.16220.00410.00590.7277-0.1377-0.00391.04220.03361.2302138.248485.7121-44.089
1006.0068-3.6368-4.8787.17011.17934.5942-0.1064-1.7644.97570.3552-0.4576-0.7135-2.6080.57120.59321.5994-0.15120.26790.7956-0.26662.0192181.0438139.8207-63.7158
1016.17183.80982.03133.52162.65532.4268-0.60520.40121.6516-0.434-0.03310.444-0.959-0.30210.62251.98180.13640.25491.18530.09691.8232175.1267140.8427-71.9223
1023.4652-2.0571-3.12235.5653.74833.639-0.06651.14310.984-0.6773-0.29950.7775-0.9275-1.02670.30941.01440.57630.07531.72250.33551.0434172.8204129.0468-76.5567
1039.17454.72196.72258.06713.63236.50240.39591.72841.8033-1.57880.2075-1.5113-1.36431.3096-0.62070.9730.35160.57721.00490.39981.4503181.6267132.9247-74.1737
1046.2379-4.929-5.84463.92744.71155.74150.2399-0.42360.5135-0.08680.3518-2.8113-0.30183.1336-0.59430.66360.0877-0.00031.40210.03661.2167186.8392128.2925-65.6991
1057.4646-2.2716-3.58997.34852.1814.22730.56310.04630.7096-0.14310.45820.2321-0.7011-0.0836-0.980.81490.0420.20661.10120.22370.6373176.0724126.953-66.8099
1062.94851.5972.5672.50670.34382.90.29940.31860.350.12290.1271-1.20320.22920.7454-0.40280.8030.50470.13541.52450.18241.2499193.2369125.7966-70.6526
1076.65980.7389-3.37615.2581-4.3114.7269-0.15641.0325-1.4162-1.39120.55790.57712.1298-2.219-0.38481.3459-0.2264-0.61362.0866-0.45181.9322252.4158113.332727.7244
1082.3121.94190.41711.63280.25253.7578-0.5918-1.6972-0.15781.58750.4689-0.3031-0.3286-1.03820.10721.93670.6871-0.54843.34520.2131.5365251.987999.767742.2742
1097.38976.9809-6.40767.9186-4.29397.8957-0.5656-0.96080.23211.31920.1463-1.9171-0.02831.13350.41491.3975-0.2006-0.11662.4516-0.14251.6258247.036793.225137.2863
1100.19170.63960.14512.13340.48430.1099-0.2483-1.31560.57621.03580.0439-0.5631-0.31610.03310.23251.14130.0073-0.22613.2399-0.1890.9068247.8059105.005129.5588
1115.65241.62752.11515.0383-0.1662.92220.3907-1.2626-0.8070.69240.2268-0.95480.24331.0418-0.59741.1176-0.0025-0.182.2410.01241.2069250.716296.788829.1057
1124.4295-1.48265.20362.1509-1.31456.2206-0.4922-0.2588-0.07470.58340.3275-0.8028-0.46451.42570.14071.3809-0.2176-0.13011.58160.05291.464242.20997.391718.0642
1132.9133-0.34123.62251.9271-0.43897.35780.3621-0.0764-0.2989-0.150.20920.49831.0225-0.167-0.60871.031-0.1080.09790.57150.16071.0469108.084241.8881-19.6453
1140.0297-0.0097-0.01460.00850.0190.04780.24-0.654-0.0040.8430.20041.0837-0.0388-0.3291-0.43950.9828-0.08780.04341.04070.40821.2924105.664851.4786-14.7462
1151.94012.54581.84555.07153.2964.0736-0.26160.80580.4156-0.48790.4881-0.1505-1.53571.06-0.23371.2568-0.5101-0.01071.09960.52731.6307103.345152.1199-31.225
1165.0823-5.9474-4.77239.67733.73975.7341-0.03150.747-0.908-0.4243-0.72141.67171.2822-2.24590.6491.2744-0.4459-0.25451.54120.09751.310592.939347.7888-38.8206
1177.9137-3.0295-1.11951.6840.9591.2554-0.3357-0.88280.87131.41820.0969-0.2884-0.80960.74750.24551.2067-0.2322-0.0181.9355-0.94241.7934251.952125.04572.8101
1188.8742-7.29495.74358.9395-1.27488.28140.03680.0070.4296-0.83180.0849-1.1456-0.09480.8954-0.10920.8951-0.09170.27791.3455-0.78681.8168248.3542129.94094.3806
1198.55721.95591.22062.2694-1.13348.23550.0402-1.00360.88870.6972-0.59190.0781-0.8601-0.03860.51761.0068-0.1508-0.17522.525-1.09731.7869254.1537133.397210.7119
1203.44524.29992.8738.5937-0.24677.08160.502-0.95720.8287-0.04090.4027-0.8073-0.18721.032-0.86571.55920.5258-0.11863.0311-0.55422.4391193.573799.1599-0.7262
1214.12182.8028-0.91053.2053-2.56273.11360.1116-1.0494-0.00290.55110.2375-3.57050.80062.8714-0.33721.52850.6201-0.32633.3882-0.57133.264203.435694.59635.2126
1228.20320.40891.13146.6943-5.2644.39650.3483-1.20783.25912.50221.1655-0.3314-2.09931.5171-1.5882.2643-0.24650.45962.2147-0.56412.3257184.2864126.2336-39.0763
1231.99991.43395.19391.9998-0.34072.60081.13162.5074-1.3305-1.6725-1.317-3.33351.58442.70780.18641.03950.7697-0.15391.7191-0.13941.7447203.4825102.2805-19.7687
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:920)A5 - 920
2X-RAY DIFFRACTION2chain 'A' and (resseq 921:1400)A921 - 1400
3X-RAY DIFFRACTION3chain 'A' and (resseq 1401:1532)A1401 - 1532
4X-RAY DIFFRACTION4chain 'A' and (resseq 1533:1541)A1533 - 1541
5X-RAY DIFFRACTION5chain 'B' and (resseq 7:25)B7 - 25
6X-RAY DIFFRACTION6chain 'B' and (resseq 26:64)B26 - 64
7X-RAY DIFFRACTION7chain 'B' and (resseq 65:86)B65 - 86
8X-RAY DIFFRACTION8chain 'B' and (resseq 87:122)B87 - 122
9X-RAY DIFFRACTION9chain 'B' and (resseq 123:148)B123 - 148
10X-RAY DIFFRACTION10chain 'B' and (resseq 149:226)B149 - 226
11X-RAY DIFFRACTION11chain 'B' and (resseq 227:240)B227 - 240
12X-RAY DIFFRACTION12chain 'C' and (resseq 2:112)C2 - 112
13X-RAY DIFFRACTION13chain 'C' and (resseq 113:207)C113 - 207
14X-RAY DIFFRACTION14chain 'D' and (resseq 2:34)D2 - 34
15X-RAY DIFFRACTION15chain 'D' and (resseq 35:67)D35 - 67
16X-RAY DIFFRACTION16chain 'D' and (resseq 68:148)D68 - 148
17X-RAY DIFFRACTION17chain 'D' and (resseq 149:181)D149 - 181
18X-RAY DIFFRACTION18chain 'D' and (resseq 182:209)D182 - 209
19X-RAY DIFFRACTION19chain 'E' and (resseq 5:14)E5 - 14
20X-RAY DIFFRACTION20chain 'E' and (resseq 15:27)E15 - 27
21X-RAY DIFFRACTION21chain 'E' and (resseq 28:50)E28 - 50
22X-RAY DIFFRACTION22chain 'E' and (resseq 51:63)E51 - 63
23X-RAY DIFFRACTION23chain 'E' and (resseq 64:79)E64 - 79
24X-RAY DIFFRACTION24chain 'E' and (resseq 80:86)E80 - 86
25X-RAY DIFFRACTION25chain 'E' and (resseq 87:103)E87 - 103
26X-RAY DIFFRACTION26chain 'E' and (resseq 104:140)E104 - 140
27X-RAY DIFFRACTION27chain 'E' and (resseq 141:154)E141 - 154
28X-RAY DIFFRACTION28chain 'F' and (resseq 1:32)F1 - 32
29X-RAY DIFFRACTION29chain 'F' and (resseq 33:92)F33 - 92
30X-RAY DIFFRACTION30chain 'F' and (resseq 93:101)F93 - 101
31X-RAY DIFFRACTION31chain 'G' and (resseq 2:11)G2 - 11
32X-RAY DIFFRACTION32chain 'G' and (resseq 12:20)G12 - 20
33X-RAY DIFFRACTION33chain 'G' and (resseq 21:52)G21 - 52
34X-RAY DIFFRACTION34chain 'G' and (resseq 53:57)G53 - 57
35X-RAY DIFFRACTION35chain 'G' and (resseq 58:79)G58 - 79
36X-RAY DIFFRACTION36chain 'G' and (resseq 80:92)G80 - 92
37X-RAY DIFFRACTION37chain 'G' and (resseq 93:109)G93 - 109
38X-RAY DIFFRACTION38chain 'G' and (resseq 110:129)G110 - 129
39X-RAY DIFFRACTION39chain 'G' and (resseq 130:144)G130 - 144
40X-RAY DIFFRACTION40chain 'G' and (resseq 145:156)G145 - 156
41X-RAY DIFFRACTION41chain 'H' and (resseq 1:18)H1 - 18
42X-RAY DIFFRACTION42chain 'H' and (resseq 19:29)H19 - 29
43X-RAY DIFFRACTION43chain 'H' and (resseq 30:41)H30 - 41
44X-RAY DIFFRACTION44chain 'H' and (resseq 42:53)H42 - 53
45X-RAY DIFFRACTION45chain 'H' and (resseq 54:62)H54 - 62
46X-RAY DIFFRACTION46chain 'H' and (resseq 63:72)H63 - 72
47X-RAY DIFFRACTION47chain 'H' and (resseq 73:85)H73 - 85
48X-RAY DIFFRACTION48chain 'H' and (resseq 86:95)H86 - 95
49X-RAY DIFFRACTION49chain 'H' and (resseq 96:100)H96 - 100
50X-RAY DIFFRACTION50chain 'H' and (resseq 101:106)H101 - 106
51X-RAY DIFFRACTION51chain 'H' and (resseq 107:116)H107 - 116
52X-RAY DIFFRACTION52chain 'H' and (resseq 117:127)H117 - 127
53X-RAY DIFFRACTION53chain 'H' and (resseq 128:138)H128 - 138
54X-RAY DIFFRACTION54chain 'I' and (resseq 2:25)I2 - 25
55X-RAY DIFFRACTION55chain 'I' and (resseq 26:32)I26 - 32
56X-RAY DIFFRACTION56chain 'I' and (resseq 33:53)I33 - 53
57X-RAY DIFFRACTION57chain 'I' and (resseq 54:88)I54 - 88
58X-RAY DIFFRACTION58chain 'I' and (resseq 89:97)I89 - 97
59X-RAY DIFFRACTION59chain 'I' and (resseq 98:117)I98 - 117
60X-RAY DIFFRACTION60chain 'I' and (resseq 118:128)I118 - 128
61X-RAY DIFFRACTION61chain 'J' and (resseq 3:29)J3 - 29
62X-RAY DIFFRACTION62chain 'J' and (resseq 30:42)J30 - 42
63X-RAY DIFFRACTION63chain 'J' and (resseq 43:47)J43 - 47
64X-RAY DIFFRACTION64chain 'J' and (resseq 48:70)J48 - 70
65X-RAY DIFFRACTION65chain 'J' and (resseq 71:78)J71 - 78
66X-RAY DIFFRACTION66chain 'J' and (resseq 79:85)J79 - 85
67X-RAY DIFFRACTION67chain 'J' and (resseq 86:93)J86 - 93
68X-RAY DIFFRACTION68chain 'J' and (resseq 94:100)J94 - 100
69X-RAY DIFFRACTION69chain 'K' and (resseq 11:34)K11 - 34
70X-RAY DIFFRACTION70chain 'K' and (resseq 35:57)K35 - 57
71X-RAY DIFFRACTION71chain 'K' and (resseq 58:75)K58 - 75
72X-RAY DIFFRACTION72chain 'K' and (resseq 76:100)K76 - 100
73X-RAY DIFFRACTION73chain 'K' and (resseq 101:110)K101 - 110
74X-RAY DIFFRACTION74chain 'K' and (resseq 111:126)K111 - 126
75X-RAY DIFFRACTION75chain 'L' and (resseq 5:32)L5 - 32
76X-RAY DIFFRACTION76chain 'L' and (resseq 33:128)L33 - 128
77X-RAY DIFFRACTION77chain 'M' and (resseq 2:14)M2 - 14
78X-RAY DIFFRACTION78chain 'M' and (resseq 15:21)M15 - 21
79X-RAY DIFFRACTION79chain 'M' and (resseq 22:61)M22 - 61
80X-RAY DIFFRACTION80chain 'M' and (resseq 62:83)M62 - 83
81X-RAY DIFFRACTION81chain 'M' and (resseq 84:93)M84 - 93
82X-RAY DIFFRACTION82chain 'M' and (resseq 94:119)M94 - 119
83X-RAY DIFFRACTION83chain 'N' and (resseq 2:11)N2 - 11
84X-RAY DIFFRACTION84chain 'N' and (resseq 12:16)N12 - 16
85X-RAY DIFFRACTION85chain 'N' and (resseq 17:24)N17 - 24
86X-RAY DIFFRACTION86chain 'N' and (resseq 25:29)N25 - 29
87X-RAY DIFFRACTION87chain 'N' and (resseq 30:61)N30 - 61
88X-RAY DIFFRACTION88chain 'O' and (resseq 2:15)O2 - 15
89X-RAY DIFFRACTION89chain 'O' and (resseq 16:49)O16 - 49
90X-RAY DIFFRACTION90chain 'O' and (resseq 50:73)O50 - 73
91X-RAY DIFFRACTION91chain 'O' and (resseq 74:88)O74 - 88
92X-RAY DIFFRACTION92chain 'P' and (resseq 1:19)P1 - 19
93X-RAY DIFFRACTION93chain 'P' and (resseq 20:43)P20 - 43
94X-RAY DIFFRACTION94chain 'P' and (resseq 44:52)P44 - 52
95X-RAY DIFFRACTION95chain 'P' and (resseq 53:62)P53 - 62
96X-RAY DIFFRACTION96chain 'P' and (resseq 63:83)P63 - 83
97X-RAY DIFFRACTION97chain 'Q' and (resseq 2:17)Q2 - 17
98X-RAY DIFFRACTION98chain 'Q' and (resseq 18:82)Q18 - 82
99X-RAY DIFFRACTION99chain 'Q' and (resseq 83:100)Q83 - 100
100X-RAY DIFFRACTION100chain 'R' and (resseq 19:23)R19 - 23
101X-RAY DIFFRACTION101chain 'R' and (resseq 24:28)R24 - 28
102X-RAY DIFFRACTION102chain 'R' and (resseq 29:36)R29 - 36
103X-RAY DIFFRACTION103chain 'R' and (resseq 37:43)R37 - 43
104X-RAY DIFFRACTION104chain 'R' and (resseq 44:52)R44 - 52
105X-RAY DIFFRACTION105chain 'R' and (resseq 53:76)R53 - 76
106X-RAY DIFFRACTION106chain 'R' and (resseq 77:88)R77 - 88
107X-RAY DIFFRACTION107chain 'S' and (resseq 2:12)S2 - 12
108X-RAY DIFFRACTION108chain 'S' and (resseq 13:25)S13 - 25
109X-RAY DIFFRACTION109chain 'S' and (resseq 26:35)S26 - 35
110X-RAY DIFFRACTION110chain 'S' and (resseq 36:40)S36 - 40
111X-RAY DIFFRACTION111chain 'S' and (resseq 41:70)S41 - 70
112X-RAY DIFFRACTION112chain 'S' and (resseq 71:81)S71 - 81
113X-RAY DIFFRACTION113chain 'T' and (resseq 8:66)T8 - 66
114X-RAY DIFFRACTION114chain 'T' and (resseq 67:75)T67 - 75
115X-RAY DIFFRACTION115chain 'T' and (resseq 76:91)T76 - 91
116X-RAY DIFFRACTION116chain 'T' and (resseq 92:106)T92 - 106
117X-RAY DIFFRACTION117chain 'U' and (resseq 2:8)U2 - 8
118X-RAY DIFFRACTION118chain 'U' and (resseq 9:15)U9 - 15
119X-RAY DIFFRACTION119chain 'U' and (resseq 16:25)U16 - 25
120X-RAY DIFFRACTION120chain 'V' and (resseq 1:4)V1 - 4
121X-RAY DIFFRACTION121chain 'W' and (resseq 32:40)W32 - 40
122X-RAY DIFFRACTION122chain 'a' and (resseq 31:41)a31 - 41
123X-RAY DIFFRACTION123chain 'b' and (resseq 1:2)b1 - 2

+
万見について

-
お知らせ

-
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

-
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

+
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

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