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- PDB-6cap: Crystal Structure of 30S ribosomal subunit from Thermus thermophi... -

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基本情報

登録情報
データベース: PDB / ID: 6cap
タイトルCrystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with Sisomicin
要素
  • (30S ribosomal protein ...) x 19
  • 16S Ribosomal RNA rRNA
  • RIBOSOMAL PROTEIN S5
  • RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3')
  • RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')
キーワードRIBOSOME (リボソーム) / translation (翻訳 (生物学)) / miscoding / antibiotic (抗生物質) / sisomicin
機能・相同性
機能・相同性情報


small ribosomal subunit / tRNA binding / rRNA binding / リボソーム / structural constituent of ribosome / 翻訳 (生物学) / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / 細胞質
類似検索 - 分子機能
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 S7 / Ribosomal protein S7/S5 ...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 S7 / Ribosomal protein S7/S5 / Ribosomal protein S6/Translation elongation factor EF1B / Ribosomal protein S3 C-terminal domain / Helix hairpin bin / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / K homology (KH) domain / Helicase, Ruva Protein; domain 3 - #50 / Glucose-6-phosphate isomerase like protein; 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 / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / KHドメイン / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / : / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KHドメイン / Few Secondary Structures / イレギュラー / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S17, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S13, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S14 / Ribosomal protein S2 / Ribosomal protein S4/S9 N-terminal domain / Type-2 KH domain profile. / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S13/S18
類似検索 - ドメイン・相同性
Chem-SIS / : / リボ核酸 / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 ...Chem-SIS / : / リボ核酸 / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS5 / 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 / 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 (サーマス・サーモフィルス)
Thermus thermophilus HB8 (サーマス・サーモフィルス)
手法X線回折 / シンクロトロン / 解像度: 3.4 Å
データ登録者DeMirci, H.
引用ジャーナル: To Be Published
タイトル: Crystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with Sisomicin
著者: DeMirci, H.
履歴
登録2018年1月31日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年7月25日Provider: repository / タイプ: Initial release
改定 1.12020年10月21日Group: Data collection / Derived calculations
カテゴリ: pdbx_struct_conn_angle / reflns_shell ...pdbx_struct_conn_angle / reflns_shell / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rrim_I_all / _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.ptnr2_symmetry / _struct_conn_type.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 Ribosomal RNA rRNA
B: 30S ribosomal protein S2
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 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 type Z
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
Y: RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')
W: RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)779,099278
ポリマ－772,39623
非ポリマー6,703255
水3,999222
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: equilibrium centrifugation
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)400.970, 400.970, 175.050
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 , 3種, 3分子 AYW

#1: RNA鎖 16S Ribosomal RNA rRNA


分子量: 494168.781 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: GenBank: 55771382
#22: RNA鎖 RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')


分子量: 1792.037 Da / 分子数: 1 / 由来タイプ: 合成
由来: (合成) Thermus thermophilus HB8 (サーマス・サーモフィルス)
#23: RNA鎖 RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3')


分子量: 4815.937 Da / 分子数: 1 / 由来タイプ: 合成
由来: (合成) Thermus thermophilus HB8 (サーマス・サーモフィルス)

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30S ribosomal protein ... , 19種, 19分子 BCDFGHIJKLMNOPQRSTU

#2: タンパク質 30S ribosomal protein S2 /


分子量: 26987.271 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P80371
#3: タンパク質 30S ribosomal protein S3 /


分子量: 22862.430 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P80372
#4: タンパク質 30S ribosomal protein S4 /


分子量: 24242.254 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P80373
#6: タンパク質 30S ribosomal protein S6 / / TS9


分子量: 11988.753 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q5SLP8
#7: タンパク質 30S ribosomal protein S7 /


分子量: 17919.775 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P0DOY9
#9: タンパク質 30S ribosomal protein S9 /


分子量: 14279.419 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P80374
#10: タンパク質 30S ribosomal protein S10 /


分子量: 11299.176 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q5SHN7
#11: タンパク質 30S ribosomal protein S11 /


分子量: 12319.034 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P80376
#12: タンパク質 30S ribosomal protein S12 /


分子量: 13850.402 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q5SHN3
#13: タンパク質 30S ribosomal protein S13 /


分子量: 13365.560 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P80377
#14: タンパク質 30S ribosomal protein S14 type Z / リボソーム


分子量: 7027.529 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P0DOY6
#15: タンパク質 30S ribosomal protein S15 /


分子量: 10390.160 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q5SJ76
#16: タンパク質 30S ribosomal protein S16 /


分子量: 9924.469 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q5SJH3
#17: タンパク質 30S ribosomal protein S17 /


分子量: 11721.919 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P0DOY7
#18: タンパク質 30S ribosomal protein S18 /


分子量: 8155.812 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q5SLQ0
#19: タンパク質 30S ribosomal protein S19 /


分子量: 9203.743 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q5SHP2
#20: タンパク質 30S ribosomal protein S20 /


分子量: 10921.086 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P80380
#21: タンパク質・ペプチド 30S ribosomal protein Thx / リボソーム / S31


分子量: 2960.475 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q5SIH3

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タンパク質 , 1種, 1分子 E

#5: タンパク質 RIBOSOMAL PROTEIN S5 /


分子量: 16331.079 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (サーマス・サーモフィルス)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P62665, UniProt: Q5SHQ5*PLUS

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非ポリマー , 4種, 477分子

#24: 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: 252 / 由来タイプ: 合成 / 式: Mg
#25: 化合物 ChemComp-SIS / (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside / Sisomicin / シソマイシン / Sisomicin


分子量: 447.526 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C19H37N5O7 / コメント: 抗生剤*YM
#26: 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
#27: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 222 / 由来タイプ: 天然 / 式: H2O

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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: 4.59 Å3/Da / 溶媒含有率: 73.2 %
結晶化温度: 298 K / 手法: マイクロバッチ法 / pH: 6.5 / 詳細: 17% 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: SSRL / ビームライン: BL12-2 / 波長: 0.98 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2017年4月14日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.98 Å / 相対比: 1
反射解像度: 3.12→39.908 Å / Num. obs: 244903 / % possible obs: 97.7 % / 冗長度: 97.904 % / Biso Wilson estimate: 127.69 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 1.011 / Rrim(I) all: 1.017 / Χ2: 0.769 / Net I/σ(I): 7.64 / Num. measured all: 23977077 / Scaling rejects: 6117
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Mean I/σ(I) obsNum. measured obsNum. possibleNum. unique obs% possible allCC1/2Rmerge(I) obsRrim(I) all
3.12-3.243.2180.19561839183441300070.9
3.2-3.2978.8140.441410147179671789299.6
3.29-3.3897.1550.59168671417367173611000.145
3.38-3.4998.6590.74167226316958169501000.202
3.49-3.699.1360.89162395316387163811000.39.069.105
3.6-3.7398.6761.17157229815937159341000.4227.1947.231
3.73-3.8793.4131.441428381153101529199.90.5575.7585.789
3.87-4.03105.1522.19155530114794147911000.7323.9683.987
4.03-4.21107.3862.99152412414198141931000.822.9522.965
4.21-4.41107.1333.98145593413594135901000.8912.2362.247
4.41-4.65104.9765.25135544412912129121000.9371.7081.716
4.65-4.93101.8066.61124926612275122711000.951.3561.363
4.93-5.27111.5999.16128852511548115461000.9781.0191.023
5.27-5.7110.39111.6118726010757107551000.9860.7930.796
5.7-6.24105.38213.721047915994599441000.990.6510.654
6.24-6.98107.818.529721379026901899.90.9940.4560.458
6.98-8.06109.87729.14879122800180011000.9980.2720.273
8.06-9.8799.79236.756788866824680399.70.9990.1880.189
9.87-13.95105.28157.425636755355535410010.1040.104
13.95-39.90890.49861.582638933114291693.610.0650.066

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解析

ソフトウェア
名称バージョン分類
XDSデータ削減
XSCALEデータスケーリング
PHENIX精密化
PDB_EXTRACT3.24データ抽出
PHENIX位相決定
精密化解像度: 3.4→39.908 Å / SU ML: 0.53 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 25.91
Rfactor反射数%反射
Rfree0.2298 1580 0.82 %
Rwork0.1829 --
obs0.1833 193729 99.81 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 395.79 Å2 / Biso mean: 142.3971 Å2 / Biso min: 57.36 Å2
精密化ステップサイクル: final / 解像度: 3.4→39.908 Å
タンパク質核酸リガンド溶媒全体
原子数19088 32943 507 0 52538
Biso mean--138.39 --
残基数----3910
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00456678
X-RAY DIFFRACTIONf_angle_d0.82384131
X-RAY DIFFRACTIONf_chiral_restr0.04310527
X-RAY DIFFRACTIONf_plane_restr0.0054910
X-RAY DIFFRACTIONf_dihedral_angle_d16.93730812
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.50970.4011430.35271731317456100
3.5097-3.6350.33131410.32581730017441100
3.635-3.78050.34671430.29171734417487100
3.7805-3.95240.2861420.2641730317445100
3.9524-4.16060.2941440.2241740117545100
4.1606-4.42090.25181430.19011738717530100
4.4209-4.76180.21221430.17311744917592100
4.7618-5.240.19481440.15231747117615100
5.24-5.9960.18981450.14131758117726100
5.996-7.5460.22641460.151767517821100
7.546-39.91070.18081460.148179251807199
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)
10.40110.1316-0.1510.4437-0.07370.32410.02580.0387-0.01640.16830.08280.14110.0837-0.0125-0.10550.94230.10130.09090.8346-0.0431.2755143.858783.602-12.7601
21.0617-0.16150.1640.4943-0.1180.32610.0897-0.58280.41470.24980.0069-0.112-0.22010.1178-0.09010.974-0.22280.14451.3922-0.51911.3214222.4408129.61569.0598
31.79520.6558-0.61340.2612-0.34070.2227-0.2251-0.0117-0.5124-0.1470.243-0.40960.16250.0747-0.01371.10340.11970.00851.1159-0.08261.4668164.771370.142-26.3445
49.244-6.70956.85844.8853-4.97815.0884-0.3159-2.70860.11621.84743.07312.3229-1.6135-0.9384-2.76682.29240.56640.45223.52160.49292.2761203.6749111.9569-33.6588
51.9693-3.2679-1.85079.28255.90155.79960.3637-0.183-0.1472-2.89070.5894-0.4213-1.40250.4196-0.93841.4768-0.1060.03860.7830.1461.5752155.4271158.0335-34.9841
66.3061-1.6316-1.41925.20875.84028.85830.75470.24720.9231-0.5875-0.5261.1494-0.6934-1.2417-0.18161.27660.04750.34050.68150.14912.0746149.55156.247-27.8866
73.8605-2.9348-3.81395.30522.47754.61960.2619-0.1231.8024-0.56720.1239-0.9804-1.92841.4168-0.48631.3252-0.12440.35271.1023-0.09161.7758166.4101162.9289-19.4978
86.78474.01190.94448.8413-2.85611.96360.2543-0.85620.4303-0.48920.0219-0.2235-0.5139-0.1566-0.2531.1040.06160.42951.0518-0.54751.6331173.7165157.9105-7.4852
96.7345-3.6646-1.06816.3484-2.2922.1532-0.6983-0.88331.83830.43880.8236-0.7607-1.5451.6275-0.08281.8972-0.46360.41251.5487-0.80932.4485189.7442163.2091-5.5855
101.9829-0.93132.7866.5854-2.88474.32680.2184-0.24470.9055-0.59290.1902-0.6488-0.74340.2365-0.32011.4460.07050.59590.7052-0.27462.1514159.7511156.734-18.9441
114.45675.8773-3.24979.1431-5.71993.84661.9989-0.11652.7775-1.2620.25240.2997-3.6734-0.3897-2.27522.9575-0.00950.37831.14960.25493.5401162.3006175.2166-23.7713
125.0839-1.1099-2.30111.8799-0.50941.8785-0.1044-0.67840.87420.54850.1787-0.36160.1393-0.0773-0.07771.4813-0.14550.02891.8661-0.78811.2323205.2191142.144533.1926
131.5984-1.86051.86549.8182-1.76852.1868-0.3154-0.98150.38590.35440.27840.1843-0.0147-0.81380.02630.899-0.16050.36352.0157-0.69211.4186189.9488133.848417.3698
144.0003-4.1472-2.01865.4742-0.48386.6142-0.0549-0.2309-0.39960.74011.40871.08760.50390.0069-1.38571.3776-0.0577-0.09950.9006-0.1021.3487154.6989111.150437.3286
152.75971.77091.60777.0825-4.05835.31960.4651-0.72781.2751-0.0789-0.3623-0.0528-0.8860.6045-0.05571.40030.05670.17710.9695-0.16361.0857160.8367113.272624.9608
162.90561.4812-0.38414.4-6.02359.5750.06160.1767-0.4160.3087-0.0477-0.0030.6294-0.3774-0.11231.28570.04960.32240.6834-0.21671.3325136.6412103.697830.9379
171.31550.9159-0.60389.1994-5.54838.27570.5027-1.37960.912.98120.29591.7864-2.164-0.1603-0.79351.6471-0.04540.46161.3706-0.32711.2299132.9523109.964147.6385
186.24630.437-6.14896.5867-0.41196.09192.21521.33922.2786-0.5033-0.4347-0.0346-2.6994-1.7366-1.73181.22340.2622-0.04011.06820.1651.0331139.9522113.995823.2672
195.1649-1.0388-4.77414.83664.34826.9349-0.8864-1.36650.68361.7149-0.15310.84410.5591-0.45620.98511.01720.06530.04451.6073-0.33551.317162.0509127.09917.8353
203.58312.0709-3.62742.65070.76919.34-0.8680.538-2.07730.3744-0.83620.5151-0.8321-2.0951.63860.91380.04620.10841.6229-0.48191.3968183.904122.9366-2.9522
211.8043-2.2879-3.50685.49262.04418.99780.8156-1.24642.93590.16430.2488-0.6792-0.33690.2969-0.98180.9418-0.19620.14240.8066-0.3261.5325162.0079129.84524.3414
227.4699-5.99582.86096.07890.68218.8017-1.3583-0.75232.89631.69610.86460.0896-1.60520.51570.48871.3772-0.2990.33090.8076-0.30791.5832167.6794133.72845.1284
231.9792.008-3.43792.711-4.66338.0351.4182-0.06974.12810.3317-0.57962.2665-0.7002-0.3758-0.95390.86560.09670.23120.9744-0.12031.8146145.1938129.20340.2796
242.4954-1.7174-0.20565.62313.87544.0446-1.49952.505-4.7172-0.2914-0.31160.66871.2658-1.39921.77790.8852-0.05430.26781.12530.01222.1173152.575120.0736-11.0907
259.9129-6.3535-5.69764.6165.2177.7897-1.3041-0.5888-0.8716-0.58070.29240.30530.4071-0.43131.07241.22140.01180.38280.6387-0.27851.4236145.8277116.75380.8534
266.9486-4.2557-5.46226.39526.318.3463-0.165-0.2061-0.65440.2259-0.39120.49460.36470.39970.50860.757-0.09490.21060.7384-0.18690.83153.4433120.7782-0.5707
274.9905-5.10454.75695.2329-4.86784.5428-0.5703-0.01261.88721.2681-0.62210.0323-1.1315-1.34141.0161.23460.29180.28990.9852-0.18351.9571136.3975133.822-9.329
289.67440.8481-5.14618.95740.84084.3223-0.61092.1164-0.8201-1.4404-0.18280.32070.3696-0.10010.86831.41830.0962-0.16341.8855-0.16440.8107173.9745114.8821-94.1886
296.97042.16775.51578.33983.82346.7620.36111.6235-0.2639-0.7868-0.1854-0.7192-0.32160.6516-0.18530.96520.0590.22141.23730.07290.7961174.7905115.9589-87.6461
304.26422.23545.05753.62943.04396.0629-2.0894-0.8672.8127-2.9519-0.47255.2363-2.6791-1.79642.50151.31640.1202-0.47491.68580.41822.4539165.6612131.7217-74.23
316.10046.4855-4.16087.1621-4.78783.34431.1693-0.7945.28830.7286-0.86013.3879-1.5387-0.3782-0.40321.25070.01090.12381.012-0.39322.1766217.4626143.2876-24.0617
326.51815.413-2.45154.5026-2.05210.97640.5348-0.5933.8783-0.4028-0.2334-1.573-1.41050.0394-0.24641.52580.01080.19720.8555-0.12852.4119239.3934152.2425-25.6771
337.6519-6.78270.42646.7637-3.02319.608-0.9169-0.75341.06360.64250.2977-0.6764-0.96910.39850.60241.1236-0.17450.00811.1775-0.5111.6001245.0735142.9364-23.3561
345.54882.7301-5.06095.69230.11927.221-0.14940.64041.0914-1.3764-0.09850.9106-0.95421.12720.2011.7347-1.00270.35781.92030.17192.1793254.0761146.1762-37.6603
359.6976.1635.89017.07464.5883.80640.150.34791.7033-0.4289-0.52721.32470.2119-0.68780.48080.97-0.02690.2071.52660.14111.1772233.1255136.447-38.2391
365.08885.06394.96585.04454.9754.91461.3451-2.0352-1.15382.701-1.15-0.13772.3635-0.4216-0.26371.87830.15080.09071.43480.36181.0728219.4913124.6962-39.1679
376.34151.18212.09822.85713.2184.74840.2337-0.6643-2.17790.3895-0.48380.79210.6645-1.52390.14361.1054-0.47350.41661.092-0.09012.0225234.9289135.6456-31.4429
389.1559-9.13396.81789.7338-6.90935.10360.03581.42360.19710.05790.1363-0.43350.02632.1699-0.09830.9566-0.23130.39791.1735-0.20021.632250.7044134.0124-31.1673
397.84732.8888-0.90913.5054-2.84142.8656-0.64293.6206-4.7387-0.48480.6604-1.57692.63130.42260.01491.53090.10090.07241.3161-0.39991.4927237.7322128.4601-41.0397
406.5279-6.7691-6.20757.01886.43465.90441.4619-4.17576.23441.0434-0.0130.2713-2.10180.7866-1.50621.46-0.17560.35051.6894-0.65962.1895219.3297125.4372-45.1171
417.8099-0.5514-3.68259.3960.12428.98750.2557-0.6701-0.9258-0.88870.5668-0.39050.75131.3069-0.8130.81190.21370.14850.82760.0721.0911139.8569122.8991-30.9769
426.786.8636.75456.99096.8596.7487-0.0741-0.53341.4418-0.6049-0.54711.4363-1.5313-1.1950.66871.10470.33910.28991.12230.10851.3815138.8703132.5896-32.1679
435.81255.78064.69639.71256.71435.3479-0.5949-0.4690.67270.3654-0.45532.5648-0.6749-2.52111.00240.79890.27520.3431.07630.33731.6875126.3605125.8428-27.7545
449.2175-1.45463.79584.02451.38222.5976-0.7958-0.10750.5721-0.2183-0.14972.2993-2.4444-1.60850.87531.36140.195-0.06210.68450.07721.7928130.208133.2805-30.1705
453.25962.94334.38056.20362.53086.51890.0810.63250.6721-0.22310.3499-1.4935-0.30060.3197-0.41690.78220.17540.15550.98820.11161.6992133.2215132.0958-38.9583
467.9396.45885.90765.25884.81114.3910.4732-0.41040.07491.14330.43120.17880.59190.1969-0.84781.08120.02030.25230.9368-0.14112.0264145.2348140.257-17.1181
475.2415.35926.08085.48756.23427.04160.1743-1.25180.8151-0.6203-0.84580.811-0.0252-0.4540.65270.97670.15890.10850.7922-0.0461.1764143.2507129.5568-18.9657
489.76695.4091-5.15223.048-2.30118.1274-1.12390.642-0.56230.06840.2722-1.52340.68660.7950.8050.78820.10980.18710.95080.09621.2631133.8402108.9791-24.6862
492.3973-0.33420.01812.1897-0.70542.2984-1.72290.4607-5.9563-1.00880.75150.15724.63491.26651.0071.24140.07070.2060.9334-0.18581.8567125.261109.7011-12.8876
505.34935.22456.86525.10766.7128.82130.4532-5.04460.40191.5232-2.5794-2.6662-0.6803-3.28752.15471.1978-0.0524-0.19691.7751-0.04641.3646134.1124119.4094-8.4823
510.15220.10340.84713.74414.61989.2596-0.4258-1.159-0.91610.65720.10560.77990.5022-0.03860.3250.81510.24920.24071.01180.27971.3812126.1548118.8056-19.1471
529.08541.8222-5.36592.2803-0.34633.5420.48270.32581.8660.5459-0.561-1.6516-1.7829-0.50930.11010.89070.25340.05980.8480.13521.6739122.3385120.0108-15.8368
533.31763.65440.32224.04720.74659.93321.40460.0519-2.89660.0221-0.942-2.85910.52020.6207-0.5170.76350.2026-0.00060.86280.35711.5235131.0829117.3829-19.2143
544.5002-3.4113-1.27933.22432.70185.060.7585-0.51431.1555-0.5261-0.3502-0.8607-1.82150.6154-0.38141.5615-0.44180.561.3516-0.70142.3812239.6085166.8464-5.2519
550.7014-0.72371.48323.2895-3.9866.94580.24810.1237-0.70671.9059-0.6661-2.4078-1.28111.31160.26921.5154-0.7485-0.28881.3977-0.77072.0702250.3328161.8688-4.2419
568.44353.36232.18924.2137-2.63444.879-0.56210.71210.3159-0.4976-1.3477-0.76240.75241.05361.81460.94-0.16140.43671.319-0.34391.8257245.0515158.7007-13.997
575.9361-5.01553.76297.7376-5.1599.3954-0.16470.07431.76421.2384-0.414-0.2032-1.24030.93870.60121.1756-0.35340.01871.056-0.44922.0592239.8638164.82-8.9874
585.7838-3.8794-1.24335.89714.69564.7928-0.07290.42342.1967-0.7091.3621-0.2457-2.11190.9869-1.22451.3309-0.16480.30851.3448-0.44432.7819229.8938172.6573-17.7894
593.94311.52151.19839.2726-0.76310.6-0.0365-0.51831.25191.14090.15110.2302-0.4009-0.1585-0.13631.1096-0.08960.271.8019-0.66191.7412225.9967147.6119-6.8234
606.8079-6.20313.88818.8768-2.00567.6170.31131.2863-1.3047-0.89220.2716-1.9311.1486-0.6576-0.66711.1552-0.078-0.03781.8354-0.76421.7539222.2783124.4771-7.2693
618.17346.1375.38655.20453.55263.9608-0.4902-0.24550.20130.15740.94210.0425-0.91851.0799-0.46631.2805-0.22550.12611.9961-0.78951.7783222.2281162.960626.441
625.4814-0.651-5.41260.13391.04639.73111.32550.26262.0264-0.81542.9714-4.8587-2.56082.6359-4.20091.2821-0.18490.67711.8096-0.85352.5721228.2183166.534422.2618
638.11835.9426.29165.58125.26685.23010.6465-2.53631.42791.8912-0.45291.8258-0.6859-0.3169-0.19271.5456-0.05270.59932.0247-0.16251.5141225.177142.656516.8578
641.8973-0.1417-1.21691.0008-2.00985.2279-0.95311.0784-0.9928-3.03241.7495-2.8278-0.189-0.4397-0.82781.2608-0.21750.40171.583-0.60751.4225218.1551135.857612.6675
654.31222.08063.41354.8731-2.97938.237-0.2477-1.03771.76532.0574-1.07360.2366-1.6298-0.47341.41032.1047-0.9781-0.37492.4549-1.25822.5167231.1199170.028530.0967
663.3889-3.2611-3.46165.93083.17654.7911-0.1938-1.64442.1221.92550.9499-0.2531-2.2321-0.3746-0.79592.35890.8440.75162.179-1.09132.4618223.3086172.317538.3753
673.55921.31050.96351.9346-0.91791.37090.7878-4.51382.84333.2906-0.38612.0036-2.8079-2.5092-0.28381.98270.23930.66643.0214-1.13822.604215.9692161.00234.7208
681.4938-2.1615-2.91739.91833.53535.8692-0.50781.943-1.82061.61390.7776-1.4418-0.22692.837-0.21192.01260.1484-0.6122.4119-0.71071.8983228.0035156.996332.6807
695.5908-3.79396.02552.9315-4.67587.61490.16831.74220.0806-0.46310.4975-0.5933-0.742-0.9555-0.70070.8943-0.17610.42391.1466-0.13511.2569213.104118.8565-69.8522
708.0915-1.14041.78066.8466-5.37794.35650.2763-0.87130.05960.15120.11560.3822-0.47921.251-0.40370.99080.01360.25681.0808-0.24621.0384217.2412115.208-63.2167
715.17132.501-3.47276.74420.02832.91170.3842-0.11310.18730.1042-0.1705-1.56880.29511.3462-0.19550.91510.1136-0.01661.01470.15461.5562221.2418122.0929-65.136
724.38256.23941.39169.15320.83076.741-0.1528-0.79491.2174-0.161-0.93690.2087-0.21690.16061.10181.0024-0.04340.08921.1878-0.08371.432211.416126.1092-65.2326
732.674-4.95962.11739.4335-2.54729.4859-0.66481.2766-1.35060.2096-0.9351-3.0217-0.57571.00581.65620.9191-0.16380.05630.99760.07361.5916211.0024129.9909-70.3636
747.09242.73820.2349.969-4.74477.34440.59210.9757-0.4511-0.1104-0.7259-1.09710.182-0.0110.04611.10280.10220.1761.1572-0.31251.5635193.6468110.6417-58.0606
756.8548-7.30828.02377.9627-8.57279.3770.58340.6321-0.0855-0.1733-0.3156-0.16390.60010.4022-0.27510.76130.02750.00170.9963-0.05141.1413153.359189.144-14.2776
769.1641.6785-6.18632.8971.30787.1104-0.20710.2442-0.5520.21620.0907-0.48180.75860.8890.12080.96840.2766-0.15270.91830.04061.1584174.450679.27329.7793
773.896-0.53493.35333.4888-2.9425.3719-0.2119-0.8046-2.2333-1.7082-0.04693.33531.6471-1.23990.0881.2845-0.1269-0.06451.5152-0.40222.4411273.5312115.3353-8.8622
789.598-6.39043.93055.779-5.76268.2228-0.5308-0.56661.13771.37820.84431.2416-0.5863-0.107-0.33671.08860.7803-0.20921.2742-0.21191.5601268.0356119.7031-5.8007
797.7215.0653-5.31455.3922-4.86054.5706-0.2903-0.7208-0.16770.8252-0.838-1.9924-0.77420.54061.23030.934-0.1092-0.15171.4759-0.19571.6758275.4455121.3883-1.5608
805.88635.5738-4.65815.3051-4.09527.63150.7818-1.8426-1.72812.1047-0.9004-2.6922-1.18121.72670.14271.068-0.0099-0.3841.739-0.1841.1788264.4758104.23528.842
815.5468-6.03555.79746.5641-6.30596.05540.1138-1.1124-0.86190.14530.06410.381-0.1274-0.1185-0.25930.8358-0.09150.05092.2863-0.2691.687248.772998.907613.7265
824.57341.70194.25387.28423.69649.2705-0.9868-0.3116-0.2837-0.19940.23280.41270.01280.51530.76690.7462-0.23620.18211.55190.12021.4224239.9236103.51852.1695
834.39793.9079-5.48424.0116-5.20377.03710.6496-4.50072.69223.6929-0.92380.677-2.0991-1.45490.28751.60380.21590.02161.8072-0.62421.3116219.6804117.858733.7806
846.1037-4.4832-4.7855.19662.23785.5267-0.20181.1534-3.20540.0902-1.57158.8984-1.4212-4.3621.6861.49940.0342-0.09882.3022-0.29372.7169232.0686119.297537.731
853.8454-2.48354.65113.1272-1.71426.7137-0.06221.37310.76890.596-0.33110.43160.1650.2380.46241.2903-0.59430.1272.2859-0.30991.3292227.7923121.859829.9492
866.4850.5084-3.22529.03734.99994.66852.680.2459-1.1139-0.4183-1.5461.6893.8225-1.244-1.1031.206-0.1255-0.43361.6396-0.30241.3039214.9718125.473126.2327
875.11481.51551.53155.8869-0.98189.236-0.1582-0.74311.17250.2856-0.25570.18010.06720.02030.40510.8678-0.22580.20261.4711-0.62931.2792216.4766135.006119.6246
884.70396.0701-4.96399.5501-3.8749.5318-0.82764.36510.553-2.0071.0240.109-0.6205-1.0582-0.1861.27920.3473-0.08241.8776-0.0190.7718141.4755111.1447-74.7296
893.4893-5.0723-4.84248.16235.65658.78751.00961.42191.2815-1.37110.0296-0.3781-0.5697-0.2878-0.97871.1259-0.03080.04591.1140.21521.0229144.9141104.5781-67.1925
906.8512-6.0009-6.56456.34756.34637.3673-0.1738-4.474-2.04650.15560.74950.22940.62440.9551-0.47290.96070.064-0.13261.35420.37740.9692143.6606102.0931-56.827
916.02242.2835-4.05725.14832.23426.05-0.36081.582-2.36020.48080.33310.47121.9256-2.6385-0.01671.1896-0.3081-0.37871.46250.17261.7252130.947698.0052-64.2838
928.4402-1.41961.27850.7735-0.55170.4435-0.09460.01670.02490.7477-0.01730.0370.3814-0.07670.11381.358-0.02480.55060.8991-0.10711.2275118.144776.948415.1536
936.322.17074.73365.47764.55517.5605-0.01760.09641.5717-0.09140.25510.134-0.77760.5132-0.26780.9613-0.10810.31630.7181-0.04651.6234115.626177.425410.6372
945.61572.98214.18429.50426.5756.462-0.38940.02223.1989-0.58110.09780.6674-4.44450.14410.23951.818-0.00750.81020.83560.08811.8794110.290886.652920.6611
956.03646.31921.69976.61431.79245.8758-0.65520.12660.6863-1.43110.22641.6855-2.4767-0.52650.40371.46640.37620.2781.11030.88992.1026101.315879.47325.8551
969.2691-5.812-2.1449.26174.6852.4858-0.5836-1.1754-2.93792.4707-0.30811.97010.0651-0.12881.00221.5863-0.15680.58621.05630.26771.659101.814775.146416.6655
979.93398.47070.68578.2641-1.92256.5188-0.21490.79210.0019-1.10860.3010.2065-0.5388-0.1601-0.05630.59010.0498-0.11160.61310.15841.1446120.06781.0126-38.4681
980.4072-0.8766-0.09952.09810.1172.44590.0196-0.0887-0.1015-0.22810.15580.67710.3745-0.1882-0.17990.7495-0.11780.06770.91950.15041.3118122.081884.8724-35.7
994.2853-5.67414.88537.961-5.40018.24040.22951.4930.4348-0.5917-0.0808-0.7463-0.60771.4795-0.1611.0257-0.23310.11461.2203-0.16511.166138.14485.8894-44.8932
1007.24221.6156.14931.60941.68635.3673-1.1674-3.85467.96080.13260.0120.6635-3.4716-1.54531.14711.55580.31460.30651.5031-0.28832.5653180.333140.2588-64.1952
1017.25496.07777.11675.78696.21977.0778-2.1193-2.53818.18230.6350.01371.3131-5.2103-2.17522.07622.6270.34470.96391.6785-0.09933.2173175.1464141.8437-72.0721
1023.3866-5.1217-2.73728.78281.90137.0711-0.1335-0.1499-0.3805-0.1553-0.7151-1.4382-0.15310.50890.86071.04360.07710.05241.61650.17851.9468172.5125129.2946-77.3066
1036.97441.81456.30222.34314.429.82260.641.50432.871-2.4201-1.1112-2.2427-3.5853-0.70360.42421.1960.53050.50750.75160.44311.9535181.4795133.3577-75.1493
1046.0579-5.8011-4.59025.56234.47144.19521.215-0.45182.06020.09340.6776-4.6131-0.68484.5158-1.85560.81640.0510.0751.7541-0.53261.624186.6216128.8092-66.6676
1054.7224-5.2524-3.05919.56647.16325.7710.7378-0.49140.3016-0.28920.0181-0.547-0.4529-0.7305-0.75021.024-0.01090.14961.12960.27990.9894175.8442127.2688-67.6324
1069.39281.17973.90090.5289-0.19513.0002-0.0675-0.3107-0.30.2620.1061-0.31780.05360.4002-0.03781.35020.24590.04531.4162-0.01811.6275193.0878126.1664-71.2843
1070.21821.1553-1.07086.0034-5.39556.373-0.8513.6611-1.0241-2.15760.67721.38133.4008-3.84460.16711.3948-0.2794-0.1832.2328-0.45731.3415251.8598113.069827.8657
1085.6593-5.8724.1356.2146-4.46083.2565-3.2144-4.3682.55275.94151.6827-1.6769-2.64260.79631.4022.08960.1014-0.3732.1777-0.40921.4431250.8109100.073542.2716
1091.9781-3.02333.15144.6832-4.76915.0273-0.44-0.0826-0.49260.89180.1797-0.9205-0.0552-1.28760.19720.959-0.3737-0.49442.8402-0.12082.1315246.264693.498636.8353
1102.00064.91356.98512.20443.25334.8551-1.3066-5.77672.74360.7129-0.7765-0.0649-2.7169-1.131.9591.7911-0.4702-0.4132.42020.19751.3479246.5382105.089128.706
1113.34381.19294.24418.62070.85375.4473-0.5086-1.5698-0.6809-0.28110.5704-0.764-0.58490.6973-0.1341.39590.03010.04772.09420.00251.3551249.522596.314928.808
1123.76891.30113.96757.21262.03364.7635-0.69183.0804-2.1012-1.08450.5635-1.0780.05482.15180.06971.14270.03430.34331.8869-0.25271.162241.076497.050517.8976
1133.3293-2.28763.95251.7009-2.7574.52150.3726-0.0388-0.4460.13350.29480.61470.0566-0.2253-0.71090.996-0.09740.27050.75480.21251.5287108.079742.1021-20.1431
1145.69016.2771-5.54126.9264-6.11215.40911.50430.76771.24391.30581.08912.69750.37110.894-2.53030.97260.0389-0.06621.18970.10071.0975105.770952.0239-14.8062
1159.23715.856.09395.62775.43875.7064-0.50971.24961.2464-0.8944-0.1975-0.6299-2.1082.91940.58431.046-0.19010.30111.35420.58012.0764103.319552.4457-31.6119
1165.0509-3.68331.81854.70980.84433.4570.6749-0.7844-1.286-0.5416-2.61072.71970.6207-2.24721.81641.0814-0.2112-0.07931.5290.04491.510692.72648.1442-39.6516
1175.7488-5.29724.54356.6486-2.09916.08550.68760.2014-1.62470.3592-0.26212.80810.23840.3039-0.41230.9173-0.05980.04771.3448-0.51341.9887251.2144124.5171.8791
1183.77-1.28753.52742.3212-0.53923.5503-0.8778-0.42373.1302-0.37460.32641.4018-1.066-0.02980.48121.30820.1112-0.26610.8365-0.23511.913248.0744129.60423.7792
1195.9924-1.06352.05415.82840.88837.0309-0.4234-2.57841.24723.1608-0.68-1.48-0.79840.01490.9811.888-0.6194-0.30712.2404-0.51811.3541253.9407132.92649.8847
1206.32085.4644-5.52975.0438-4.85464.86290.0414-0.27532.45840.65711.01840.6377-0.7308-0.171-0.99431.54050.231-0.64821.994-0.62442.5498191.848103.7975-1.0347
1219.2836-1.11074.73025.56921.0032.88490.31650.17620.91631.4626-0.6613-0.42131.24641.47430.34751.4450.1863-0.0562.2182-0.50721.6547205.996193.00826.4465
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 'Y' and (resseq 1:6)Y1 - 6
121X-RAY DIFFRACTION121chain 'W' and (resseq 28:42)W28 - 42

+
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

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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

+
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

+
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