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- PDB-4x64: Crystal Structure of 30S ribosomal subunit from Thermus thermophilus -

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基本情報

登録情報
データベース: PDB / ID: 4x64
タイトルCrystal Structure of 30S ribosomal subunit from Thermus thermophilus
要素
  • (30S ribosomal protein ...) x 20
  • 16S rRNA
  • RNA (5'-D(*(MA6)P*AP*AP*UP*UP*U)-3')
  • RNA (5'-D(P*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*C)-3')
キーワードRibosome/antibiotic / 30S ribosomal subunit m6A decoding mRNA modification (リボソーム) / Ribosome-antibiotic complex
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
Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / 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 S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / 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 S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / 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 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S15/NS1, RNA-binding / K homology (KH) domain / Double Stranded RNA Binding Domain - #20 / Helicase, Ruva Protein; domain 3 - #50 / 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 / Double Stranded RNA Binding Domain / 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
類似検索 - ドメイン・相同性
: / パロモマイシン / : / 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 ...: / パロモマイシン / : / 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 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 HB8 (サーマス・サーモフィルス)
Thermus thermophilus (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: 3.35 Å
データ登録者Demirci, H. / Chen, J. / Choi, J. / Soltis, M. / Puglisi, J.D.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM51266 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM099687 米国
引用ジャーナル: Nat.Struct.Mol.Biol. / 年: 2016
タイトル: N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics.
著者: Choi, J. / Ieong, K.W. / Demirci, H. / Chen, J. / Petrov, A. / Prabhakar, A. / O'Leary, S.E. / Dominissini, D. / Rechavi, G. / Soltis, S.M. / Ehrenberg, M. / Puglisi, J.D.
履歴
登録2014年12月6日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02015年11月18日Provider: repository / タイプ: Initial release
改定 1.12016年1月13日Group: Database references
改定 1.22016年1月27日Group: Database references
改定 1.32016年2月10日Group: Database references
改定 1.42017年9月6日Group: Author supporting evidence / Derived calculations / カテゴリ: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
改定 1.52019年12月25日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
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 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
a: RNA (5'-D(*(MA6)P*AP*AP*UP*UP*U)-3')
b: RNA (5'-D(P*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)785,867383
ポリマ－772,88023
非ポリマー12,986360
水4,053225
1


  • 登録構造と同一
  • ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area117210 Å2
ΔGint-935 kcal/mol
Surface area276890 Å2
手法PISA
単位格子
Length a, b, c (Å)400.496, 400.496, 175.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 Aab

#1: RNA鎖 16S rRNA /


分子量: 494170.781 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell
由来: (天然) Thermus thermophilus HB8 (サーマス・サーモフィルス)
参照: GenBank: 55771382
#22: RNA鎖 RNA (5'-D(*(MA6)P*AP*AP*UP*UP*U)-3')


分子量: 1795.204 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB8
#23: RNA鎖 RNA (5'-D(P*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*C)-3')


分子量: 3708.392 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
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: 27217.490 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: 22975.588 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
#5: タンパク質 30S ribosomal protein S5 /


分子量: 16460.193 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: Q5SHQ5
#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: Q5SHQ2, UniProt: P0DOY9*PLUS
#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: 11398.308 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: 12606.369 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: 13921.479 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: Q5SHQ1, UniProt: P0DOY6*PLUS
#15: タンパク質 30S ribosomal protein S15 /


分子量: 10447.213 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: 9995.546 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: 11722.904 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: Q5SHP7, UniProt: P0DOY7*PLUS
#18: タンパク質 30S ribosomal protein S18 /


分子量: 8497.198 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: 9260.796 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: 3089.655 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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非ポリマー , 5種, 585分子

#24: 化合物
ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E / パロモマイシン / パロモマイシン


分子量: 615.628 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C23H45N5O14 / コメント: 抗菌剤, 薬剤*YM
#25: 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: 311 / 由来タイプ: 合成 / 式: Mg
#26: 化合物...
ChemComp-K / POTASSIUM ION / カリウムカチオン


分子量: 39.098 Da / 分子数: 41 / 由来タイプ: 合成 / 式: K
#27: 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
#28: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 225 / 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: 4.55 Å3/Da / 溶媒含有率: 72.98 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 / 詳細: 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: 0.9795 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2014年7月28日
放射モノクロメーター: Liquid nitrogen-cooled double crystal, non fixed exit slit
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: 0.9795 Å / 相対比: 1
Reflection冗長度: 5.8 % / 数: 1130734 / Rmerge(I) obs: 0.119 / Χ2: 0.93 / D res high: 3.35 Å / D res low: 35 Å / Num. obs: 195543 / % possible obs: 96.4
Diffraction reflection shell
最高解像度 (Å)最低解像度 (Å)IDRmerge(I) obsChi squaredRedundancy
9.043510.0771.256.5
7.29.0410.070.9856.7
6.297.210.0720.8326.4
5.726.2910.0830.8516.7
5.315.7210.0890.8576.8
55.3110.10.8736.7
4.75510.1120.8716.2
4.544.7510.1250.8486.4
4.374.5410.1450.8566.6
4.224.3710.1740.8856.6
4.094.2210.2090.9176.7
3.974.0910.2440.9226.7
3.873.9710.2840.9686.7
3.773.8710.3430.9626.5
3.693.7710.4520.9816
3.613.6910.510.9715.8
3.543.6110.5080.9142.7
3.473.5410.6050.9182.7
3.413.4710.6830.9132.7
3.353.4110.8190.9082.7
反射解像度: 3.35→35 Å / Num. obs: 195543 / % possible obs: 96.4 % / 冗長度: 5.8 % / Biso Wilson estimate: 61.72 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.052 / Rrim(I) all: 0.13 / Χ2: 0.925 / Net I/av σ(I): 12.29 / Net I/σ(I): 8 / Num. measured all: 1130734
反射 シェル

Diffraction-ID: 1 / Rejects: 0

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.35-3.412.70.81991450.580.5490.9930.90891.4
3.41-3.472.70.68392720.620.4730.8360.91392
3.47-3.542.70.60591380.6690.4240.7440.91891.3
3.54-3.612.70.50890280.7650.3470.620.91489.9
3.61-3.695.80.5198740.8760.2250.5590.97198.4
3.69-3.7760.45293460.90.1970.4950.98192.8
3.77-3.876.50.34395210.9470.1430.3720.96294.7
3.87-3.976.70.284100460.9680.1160.3070.96899.6
3.97-4.096.70.244100300.9730.0990.2630.92299.3
4.09-4.226.70.209100160.9780.0850.2260.91799.7
4.22-4.376.60.174100450.9820.0720.1880.88599.4
4.37-4.546.60.145100400.9860.060.1570.85699.4
4.54-4.756.40.125100880.9880.0520.1350.84899.4
4.75-56.20.11293690.9880.0480.1230.87192.7
5-5.316.70.199650.9920.0410.1080.87398.2
5.31-5.726.80.089101560.9930.0370.0970.85799.8
5.72-6.296.70.083102180.9930.0340.090.85199.8
6.29-7.26.40.072100500.9940.030.0790.83298.2
7.2-9.046.70.0798570.9940.0290.0760.98595.2
9.04-356.50.077103390.9910.0320.0841.2596.4

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解析

ソフトウェア
名称バージョン分類
PHENIX(phenix.refine: dev_1938)精密化
DENZOデータ削減
SCALEPACKデータスケーリング
PDB_EXTRACT3.15データ抽出
PHENIX位相決定
精密化解像度: 3.35→34.878 Å / SU ML: 0.31 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 18.71 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2049 8615 5.04 %
Rwork0.1647 --
obs0.1668 171102 84.38 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 3.35→34.878 Å
タンパク質核酸リガンド溶媒全体
原子数19119 32875 606 225 52825
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00456717
X-RAY DIFFRACTIONf_angle_d0.82184145
X-RAY DIFFRACTIONf_dihedral_angle_d19.39626746
X-RAY DIFFRACTIONf_chiral_restr0.04110585
X-RAY DIFFRACTIONf_plane_restr0.0245156
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3502-3.38820.3136410.2901735X-RAY DIFFRACTION12
3.3882-3.4280.2617420.26461033X-RAY DIFFRACTION16
3.428-3.46980.3225860.26061516X-RAY DIFFRACTION24
3.4698-3.51370.27311140.2542258X-RAY DIFFRACTION36
3.5137-3.55990.30611630.24853001X-RAY DIFFRACTION47
3.5599-3.60860.28142050.23173608X-RAY DIFFRACTION57
3.6086-3.66010.28033040.21835917X-RAY DIFFRACTION93
3.6601-3.71470.26443440.20596138X-RAY DIFFRACTION97
3.7147-3.77260.26642860.19685754X-RAY DIFFRACTION90
3.7726-3.83440.23263280.18525821X-RAY DIFFRACTION92
3.8344-3.90040.21723860.18146286X-RAY DIFFRACTION99
3.9004-3.97130.20673660.1716324X-RAY DIFFRACTION100
3.9713-4.04750.20783030.16936360X-RAY DIFFRACTION99
4.0475-4.130.22933050.16076386X-RAY DIFFRACTION99
4.13-4.21970.2053050.15756371X-RAY DIFFRACTION100
4.2197-4.31770.19113330.15136336X-RAY DIFFRACTION99
4.3177-4.42540.19643490.14726358X-RAY DIFFRACTION100
4.4254-4.54490.18053230.14516380X-RAY DIFFRACTION99
4.5449-4.67830.18543350.13976372X-RAY DIFFRACTION100
4.6783-4.82890.17763420.13776359X-RAY DIFFRACTION99
4.8289-5.0010.17483310.13355725X-RAY DIFFRACTION90
5.001-5.20060.16913210.12756247X-RAY DIFFRACTION97
5.2006-5.43650.16233280.12556437X-RAY DIFFRACTION100
5.4365-5.72190.15463580.1276409X-RAY DIFFRACTION100
5.7219-6.07870.17053560.13646454X-RAY DIFFRACTION100
6.0787-6.54520.183190.14176459X-RAY DIFFRACTION100
6.5452-7.19860.18243500.13946323X-RAY DIFFRACTION98
7.1986-8.22830.18663080.14826091X-RAY DIFFRACTION93
8.2283-10.32210.19893550.17656579X-RAY DIFFRACTION100
10.3221-34.88030.24533290.21816450X-RAY DIFFRACTION94
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)
10.47910.1722-0.20050.3712-0.09290.3590.0467-0.01570.05250.14570.05660.08780.08230.0168-0.1080.44880.08110.03910.3817-0.02340.5197143.787683.5243-12.4602
21.3389-0.16660.10280.55180.0270.27880.0536-0.74010.48360.3144-0.0058-0.0564-0.1340.1176-0.04280.7445-0.24430.15961.2487-0.51910.7932222.138129.55619.1828
31.24320.5067-0.52870.1528-0.27740.1258-0.1794-0.1091-0.2888-0.12470.1601-0.17060.20620.00590.0270.58580.0109-0.00480.5562-0.02090.6778163.184769.3806-25.7006
49.4731-6.987-0.65935.17160.47370.05610.79291.05961.3867-1.0215-0.7332-1.4627-0.27270.9053-0.04021.30140.20170.22742.83120.29451.8393203.2408112.0472-33.4083
54.92932.74733.46424.329-1.94517.8120.37660.21671.3248-1.74460.0429-1.8602-1.04340.3103-0.39921.36410.12610.52540.6541-0.11391.392156.5905155.9548-36.3202
62.9205-1.08670.39318.94357.73098.9730.3420.2060.7585-0.8819-0.79641.1953-1.7039-1.38940.51921.04820.18070.29720.6226-0.01711.6348149.5387156.1865-28.1036
73.80820.73293.85152.596-2.12357.24430.09250.19081.3512-0.8491-0.1007-1.4604-2.11871.5498-0.00371.2469-0.23060.54320.6961-0.13291.623166.5723162.8125-19.6702
81.57571.27351.41525.79181.29595.4666-0.0241-0.14710.23270.38790.2365-0.1908-0.73250.3596-0.13891.0177-0.23170.49520.6936-0.60931.5431173.7255157.7379-7.4817
96.26842.25593.13636.8324-1.03252.3713-0.4584-0.1061.03211.02210.4556-1.0615-1.20331.67410.04441.6285-0.45780.27061.6036-0.79562.0031189.8255162.5328-5.4326
101.3167-1.25721.09133.4034-1.00582.09920.0742-0.12990.526-0.699-0.0069-0.0784-0.72930.0670.04641.21690.01220.48510.4623-0.2371.6406159.7377156.6471-19.0526
114.79284.4670.75268.7525-1.09170.81921.99140.22.2612-1.2858-0.1421-0.6561-3.5477-0.0996-1.85752.3214-0.05760.51670.87050.13352.8501162.7877174.6367-23.9352
120.5661-0.3321-0.27250.74140.1730.4185-0.0026-0.56430.21490.66050.0763-0.1195-0.06850.0157-0.13851.2193-0.16650.2991.8083-0.92250.9994204.9428142.286433.1441
130.9999-0.7182-0.79912.3820.35841.4981-0.0801-0.1603-0.04970.3469-0.0160.51840.0929-0.48650.16220.743-0.26210.41761.6083-0.88560.9823189.5906133.698717.4101
146.0201-6.4409-3.73938.18612.24845.04010.3286-0.86950.54261.3310.30290.5811-0.16520.2083-0.63490.9409-0.14810.06450.7453-0.11870.6245155.3763111.111337.7219
156.51160.17184.89963.79932.48175.60830.2659-0.29110.69380.2943-0.0995-0.5849-0.98931.0436-0.14130.9344-0.1930.09650.6498-0.15990.6376161.3304112.88825.385
162.9538-0.07890.18613.3759-2.52396.16270.255-0.13720.25150.2601-0.16370.24040.181-0.0465-0.08320.81840.02650.18590.4257-0.16090.5678137.1561103.685531.2742
174.7931-3.22822.9976.6901-2.46996.0708-0.1172-1.69970.59411.92420.34690.9479-1.2818-0.4803-0.19511.27650.03990.31460.9609-0.21930.8221133.5845109.895347.8413
187.23824.2719-6.05135.1808-4.19615.16251.11730.42071.3449-0.0438-0.08160.4235-1.5589-0.6599-1.0510.88430.17890.00350.6311-0.03580.6461140.5242113.989123.7007
195.0083-6.5429-1.7829.28873.44692.3065-0.7247-2.08411.44771.73120.35590.38890.3724-0.41220.33920.6751-0.0310.04111.3179-0.44550.8075161.7946126.9797.9223
206.7477-3.795-3.64453.39112.91862.5690.05380.00940.4253-0.00680.2843-0.6029-0.54530.855-0.30980.5865-0.18350.08040.8824-0.42110.9351183.6965122.5257-2.7299
214.1649-3.6296-4.97335.82212.43547.50220.2453-0.41680.59670.16680.07510.1938-0.22090.2941-0.32220.5568-0.1440.22690.6709-0.40520.8093161.7144129.70024.2891
225.3724-6.75814.69949.3446-5.54244.65260.0193-0.83321.36670.42390.2841-0.4323-0.7050.574-0.28150.7575-0.22820.3780.8866-0.41340.9391167.5493133.64985.1948
239.41726.78862.31856.99792.2025.95690.2155-0.64481.41650.4345-0.04610.8431-0.5436-0.2114-0.20980.57450.08740.22960.5983-0.23291.0696145.0158129.37380.3617
245.7757-3.6828-4.51876.53490.46845.2687-0.38442.7053-2.5634-0.3089-0.19780.79390.9948-1.34140.56130.46030.0370.05580.7724-0.22710.8991152.3422120.1247-10.9608
257.2133-2.5729-2.51643.14911.12894.9307-0.3761-0.2138-0.43360.33-0.12070.48810.4152-0.45040.45660.71080.0950.37640.434-0.13170.927145.4608116.85950.8627
267.1175-3.81351.55817.18942.72882.82770.0349-0.27470.16720.28930.00570.16830.177-0.156-0.03550.4723-0.03620.21250.49-0.14190.5163153.0913120.9151-0.5598
276.55262.9314.10146.08590.31934.364-0.20840.10451.7161-0.0105-0.3320.5025-1.6447-1.50440.48510.85890.3440.3070.7381-0.00451.2284136.2427133.9432-9.5435
285.93141.2805-5.4225.12720.51046.5294-0.4461.7642-0.2384-1.202-0.09220.1748-0.2662-0.52450.50880.92060.1623-0.06621.75210.1390.5304173.6662114.355-93.8234
297.9450.23554.12796.30631.45277.67440.42061.33980.1612-0.816-0.0995-0.0119-0.4778-0.1768-0.31240.69940.15130.14271.2570.15320.5007174.519115.3841-87.4946
306.61555.90315.57385.27795.01384.8495-1.1052-0.45321.7846-1.3687-0.19732.773-1.7733-1.01511.31810.90220.2589-0.06431.25240.41771.3001165.413131.4175-73.956
314.52013.6057-2.13042.8783-1.70171.00450.4694-0.79113.9430.2511-0.62352.3019-0.3916-0.69980.09640.7238-0.03920.19080.9524-0.27961.6953217.3375142.7522-23.9032
324.00482.6695-4.78987.9043-4.8946.2008-0.78730.8169-1.7568-0.1002-0.12170.33951.1537-0.97630.88980.8457-0.19430.15410.768-0.24151.5637239.1916152.03-25.6937
338.4599-3.04741.42248.3554-2.53345.905-0.2005-0.22370.7804-0.4098-0.0179-0.5274-0.60660.97550.22450.6415-0.27890.23260.7724-0.27750.984244.8499142.6847-23.5049
343.40641.8519-2.73412.68421.40857.1919-0.3540.35450.2254-0.3673-0.53640.0727-0.2713-0.26420.88161.2929-0.69150.42091.5556-0.3681.8794253.3016146.6858-37.9188
357.32044.05576.50682.84954.2716.5108-0.15391.24770.8696-0.26660.08790.41750.13370.08130.00760.62740.10550.25011.0194-0.03620.7968232.7836136.1125-38.1816
369.29586.66626.76884.80354.87244.94361.5199-1.59340.31363.02-1.3341.67720.9568-1.0075-0.18461.0988-0.05880.09961.1935-0.20880.8076219.0975124.3149-39.3293
373.7185-1.11784.01752.23380.00845.125-0.0525-0.6516-0.2651-0.1210.3620.4465-0.0032-0.5888-0.31820.5718-0.19410.250.846-0.12791.1851234.6968135.3483-31.4034
385.9143-7.05455.78288.4551-6.81535.8210.14291.2450.3741-0.6156-0.2997-0.84290.2922.07340.230.6654-0.15020.35050.8416-0.15421.0354250.2617133.8553-31.0331
395.1944.22982.20444.3847-0.76067.8958-0.76783.2063-2.4377-1.83881.1059-1.24580.90530.4251-0.3040.7063-0.06650.00431.0549-0.3350.8287237.3029127.9511-40.8439
401.8931-2.0747-2.44942.53942.56213.22590.2604-2.32992.4942.1702-0.25781.2732-2.2978-1.2794-0.03861.21120.12780.1271.4768-0.51851.1923219.1115124.9467-44.9269
419.90754.40743.04977.4047-1.42152.51340.3040.3269-0.9318-0.35040.4234-0.34650.16690.4808-0.6680.43640.1670.2220.5501-0.00690.7718139.7714122.8836-30.8287
425.1946.17413.18637.82675.72819.7234-0.19690.26420.8238-0.492-0.16480.5982-0.8553-0.28120.37390.52040.18780.29830.44920.09191.0031138.8608132.5436-32.0181
432.49310.5823-0.4548.12966.51946.3099-0.0321-0.0048-0.263-0.3413-0.81921.4627-0.8605-1.72120.83780.56150.26740.2290.63050.15281.1447126.2621125.9325-27.7696
443.563-2.2282.31817.01961.60863.17080.0087-0.2440.4348-0.51960.11020.7872-1.1736-0.8645-0.10480.63850.04340.19990.46010.01451.373130.0872133.2121-30.2007
458.4233-2.51060.34937.95822.4574.45920.51851.12570.0414-1.0481-0.6003-0.3329-0.7685-0.54190.08990.52480.26380.02530.70180.16771.0976133.0343131.9606-38.9983
464.27373.43893.31922.77142.68643.31040.0987-0.71070.9960.03760.2444-0.5701-0.5159-0.0696-0.30570.62910.17260.32770.5803-0.08911.4065145.0695140.4402-17.3406
475.18086.49215.88848.43256.73978.04130.3419-0.4127-0.20260.44480.1805-1.13140.1256-0.0601-0.52990.50820.04630.2250.4413-0.020.9683142.9969129.7427-19.0098
480.71731.0576-0.72991.5994-1.40113.3724-0.08340.06780.15680.04550.0959-0.3390.38120.4398-0.02560.40510.08630.13820.3657-0.01230.9055133.7034109.0494-24.5016
496.3667-5.19796.26636.6576-2.25769.5511-0.7444-0.4321-4.52430.2760.3161-0.0232.66271.48680.4350.53970.16870.17220.6061-0.03981.1757125.2917109.9737-12.5195
509.90514.16626.74572.33462.74974.68780.8851-0.7833-1.96851.1585-0.8856-3.50671.20310.17690.01620.7096-0.0890.04780.67070.04351.2148133.9341119.6864-9.0274
513.20390.55523.09713.52283.09394.99340.0714-0.7578-0.18630.1322-0.21210.4820.1573-0.40160.11530.47180.17150.20170.59210.08120.849125.9373118.9979-19.1697
529.0674-0.2066-3.03384.3534-2.12683.30430.019-0.84191.89650.20540.2007-0.9756-0.97890.4157-0.25370.51010.08650.2140.5544-0.03851.2163122.0764120.0631-15.7188
537.7433.7015-1.37655.52992.52714.87640.3333-0.139-0.6595-0.18240.4074-1.15170.00450.3724-0.72270.47190.17430.16360.44830.18020.9179130.9258117.4141-19.1657
542.2575-2.03851.36796.39483.34055.41780.2118-0.21360.68050.0159-0.4723-0.1505-0.95870.27410.2981.0489-0.41010.30290.9378-0.54381.8045239.2253166.6939-5.3712
550.7738-2.5252.39699.0817-7.66117.454-0.1130.30650.05461.2051-0.8051-2.2477-1.60272.0160.92020.9926-0.5177-0.06521.4873-0.62141.9951249.6876161.8132-4.6249
560.76361.6878-1.10738.525-3.90393.7798-0.39030.81590.4136-0.6494-0.1868-0.2974-0.07530.91880.55360.8662-0.38410.33311.1232-0.44931.5063244.6186158.4316-14.1358
573.82340.19262.08127.5208-1.30864.2297-0.4680.39530.63520.12030.0099-0.4619-0.98640.66950.45220.9942-0.48190.11550.7913-0.44251.6094239.3895164.6583-9.1678
582.4806-1.46250.22198.29514.96023.5122-0.16320.19091.9713-0.36310.09450.0067-1.65640.55250.05561.2523-0.2010.1370.9539-0.13991.9518229.44172.4003-17.8964
591.2799-1.65331.57565.4919-1.60442.22540.0289-0.28440.82790.4458-0.1883-0.0747-0.41410.1440.11430.706-0.38130.26731.2664-0.50991.1228225.5604147.4911-6.8392
606.5011-2.8312.46681.2365-1.25228.70630.50080.4556-0.9504-0.287-0.25720.48881.6066-0.3442-0.23440.8887-0.26990.00121.4181-0.6710.7692222.0621124.3256-7.2559
616.5855.1912.64944.63331.22332.44120.0902-0.36971.13471.0789-0.2228-0.0479-0.86860.2330.17341.2384-0.22880.06321.7712-0.93141.6568221.8423163.261926.1363
620.2832-0.27380.67790.72871.12048.3788-0.0081-0.90511.21770.4264-0.50980.7896-2.3418-0.21310.58041.574-0.50210.05271.5843-1.00632.0112227.3526166.615522.2208
638.44236.0608-2.62934.3572-1.89821.95270.0910.00940.12690.47790.07820.2132-0.33890.4722-0.18451.1064-0.07980.39741.7707-0.46631.0767224.8225142.75516.7118
640.6462-0.23370.27780.083-0.12181.9804-0.0515-0.26210.3196-0.79350.1741-0.4242-0.7523-0.0815-0.07750.9557-0.31750.30731.2865-0.57490.9114217.7481135.986812.8663
652.8229-2.76981.77737.186-3.26899.6052-0.6922-0.9850.82982.0893-0.81640.4541-2.4882-0.75771.51421.7176-0.45560.14471.9298-1.25192.0147230.7665170.244229.6511
668.1657-4.3333-7.48423.04862.77158.7817-0.1176-0.58160.30851.373-0.80981.2669-0.2809-1.42880.93892.3131-0.03320.04882.0917-1.19361.6731224.1262172.652738.4096
679.26632.86216.51724.16445.48328.84591.0003-4.98633.85122.7918-1.8692.1163-2.0015-3.59520.87581.8170.06810.54352.6529-0.74791.8957216.0097160.908734.1677
681.27771.86731.51287.08250.27912.64660.11362.1064-2.63950.65061.6341-2.7170.2442.7871-1.77351.61190.00330.01691.9616-1.03831.5953227.6092157.38732.2996
695.0607-1.77743.08139.3041-2.13822.79530.19710.74050.2518-0.6950.3759-0.3086-0.2930.1633-0.53870.345-0.04060.21650.9388-0.08530.7551212.7618118.5071-69.6183
708.3916-1.44512.43884.6093-2.78337.79250.16720.0652-0.1802-0.13380.0196-0.36770.04181.4348-0.14660.5149-0.00560.25250.7063-0.08360.6273216.9607114.7111-62.9584
718.1132.5216-1.5999.1319-3.62862.0363-0.35220.77320.5373-0.72750.0893-0.98870.2341.51740.23470.40610.05480.14370.73410.02230.7965221.0015121.7944-64.9026
723.68922.66612.82563.2946-0.46776.78940.1203-0.58510.98270.3282-0.41070.4616-0.79030.31460.27190.5974-0.07530.20870.794-0.11680.8812211.1057125.7211-65.1597
734.8318-0.85323.00834.47583.26925.212-0.47951.22870.7558-1.0964-0.4445-1.5326-0.78191.12150.92560.6573-0.08890.09430.75880.22180.7761210.6953129.429-70.1219
742.0048-1.31062.59128.5652-6.46336.3581-0.036-0.03240.15440.3080.3227-0.0531-0.4805-0.4458-0.2920.46190.10350.1690.577-0.17940.7538193.387110.3371-58.0412
752.673-4.1383.10996.4085-4.8153.59130.1669-0.1076-0.4191-0.02590.2170.24050.4355-0.0185-0.36870.39020.090.01010.6730.05520.7263153.163889.2533-13.8045
767.78860.8327-2.48935.8889-0.053.6568-0.1257-0.122-0.51520.57340.2308-0.56090.67651.0091-0.12940.50420.1576-0.16250.67240.00120.5314174.570379.14249.7639
774.7942-1.30995.53186.1275-5.34729.34440.254-0.033-1.8392-1.13750.89413.03911.2802-0.9691-1.23350.6981-0.21920.02071.6008-0.32521.5833273.0468115.1875-8.5163
784.5088-4.75794.9255.0937-5.34255.6687-0.2386-0.24861.4435-0.01020.62051.514-0.2059-0.1513-0.3750.34670.0729-0.10781.2186-0.22030.8843267.971119.6253-5.5246
796.35447.2037-4.48419.395-3.92756.26240.1919-0.7814-0.05620.2404-0.1602-0.9358-0.23550.9321-0.010.3981-0.0802-0.05341.1017-0.22180.9652275.0373121.4729-1.4655
807.61977.7038-4.9328.934-4.98115.88080.5687-1.2454-1.22040.9053-0.592-1.5373-0.540.98420.02410.6784-0.1404-0.07811.6698-0.10730.8411264.2294104.28799.0817
819.6578-6.36186.90966.9215-5.01939.28990.1664-0.2659-0.43050.6367-0.246-1.124-0.23780.91520.07170.5722-0.1389-0.02351.5013-0.19950.8006248.555798.923513.9843
823.94653.15755.14183.81563.35877.16820.05590.0255-0.43040.09010.3593-0.2750.17620.7323-0.440.5505-0.02870.00231.2279-0.20280.599239.5729103.43042.4281
833.093.62634.17424.90236.25788.90020.01420.05850.05831.20190.7662-0.7408-0.51611.1099-0.76391.2376-0.1690.22951.6415-0.66160.9977219.4912117.98333.7191
8421.99961.73451.9998-2.68711.0892-3.0383-6.76240.72986.9242.95482.02341.1236-0.28480.03961.52180.00070.241.9606-0.20160.9906231.4187119.860839.4029
858.2223-5.31823.25526.7509-2.82627.7858-0.4099-0.31540.60870.99560.3833-0.5696-0.7150.52960.03990.9514-0.40920.14191.5675-0.42930.6394227.5356121.92530.2779
862.9972-3.7299-3.7885.23044.87464.83160.05140.2246-0.06480.00410.0389-0.1590.88960.7463-0.09230.8176-0.18280.20061.443-0.38530.5458214.9148125.74826.3456
871.2068-0.9692-0.97065.10852.94216.47580.02120.00230.257-0.0058-0.07520.05140.11980.1337-0.06270.6952-0.2070.21521.1617-0.62030.7586216.1211135.137819.5977
885.5974.8365-5.55114.1855-4.92968.5996-0.26424.84771.2018-1.950.72330.1587-0.4186-0.5503-0.46320.88640.22460.10641.72140.24860.9666141.1018110.5891-74.4019
893.7605-5.60541.43479.70220.4326.62730.87451.1165-0.7397-0.9682-0.09030.6159-0.2909-0.0843-0.72760.5481-0.0073-0.09890.88320.07040.5885144.6524104.2666-66.8012
901.7996-2.52130.20625.15830.03013.01490.1077-2.5816-0.83410.42840.19470.13460.17980.3323-0.30060.43640.0333-0.05690.92180.09010.5653143.4131101.8514-56.62
914.86773.79390.48886.19563.90774.85860.70030.0784-3.04770.1522-0.77590.10551.0632-0.414-0.00110.62470.0079-0.35571.26640.17031.1603130.974597.7725-64.2327
924.8822-1.92621.86470.926-1.13812.1611-0.055-0.44610.41260.43290.07030.0111-0.1482-0.1073-0.03270.78060.050.33430.47440.03660.6837118.128376.908615.6018
931.53210.11841.12295.02681.76824.53930.1371-0.29550.6733-0.36610.1295-0.1364-0.63580.4189-0.29320.4767-0.10530.21670.4164-0.07550.8298115.648877.296611.1582
949.79926.07134.3855.12235.33537.0004-0.2234-0.23591.8575-0.4962-0.1450.1965-2.4128-0.37820.35371.02450.11580.42470.5403-0.08861.174110.475286.489821.2646
956.41662.82171.67676.65474.61833.32420.0064-0.02150.8319-0.2453-0.34781.1277-1.2855-0.75980.34720.6840.12270.31590.4490.13111.2539101.50679.54316.3023
965.67862.6274.92055.92522.14874.6149-0.1502-1.2298-0.6451.03080.14941.3736-0.0863-0.7051-0.00850.9092-0.01010.40130.57680.10331.0027101.900975.1617.156
974.27841.4198-1.16654.0612.66865.185-0.08190.57170.3928-0.74320.3650.1616-0.7021-0.0007-0.25580.6056-0.0127-0.11720.47770.21830.6259119.821281.0733-38.0672
984.1363.04440.58376.06651.35312.4305-0.37020.2461-0.0103-0.82370.4410.546-0.077-0.3891-0.05820.4669-0.09580.00090.56730.14720.5561121.835284.9243-35.2836
995.0776-0.86183.6334.6168-3.21274.10380.67652.14781.202-1.1427-0.7424-1.39430.22130.97730.08080.799-0.11770.19121.27840.08870.8778137.719585.794-44.3325
1007.1423-1.29542.72864.3236-5.97158.3773-0.10040.13653.92520.6008-0.4115-1.4701-2.92120.64540.53321.75370.01810.46950.66380.03481.3947180.707139.8535-64.2665
1013.5085-2.8676-5.47776.09793.39919.3073-0.2908-0.39290.6525-0.66610.08440.6608-0.4145-0.62280.21151.91010.40660.26210.87340.21551.6526174.8572140.8542-72.1662
1026.9186-5.099-4.02557.15995.51774.25460.20480.53750.4195-1.39450.3954-0.931-1.03990.4235-0.60490.88130.09180.19961.46820.36151.0175172.2779128.9072-77.2151
1032.814-0.3791-0.85383.22614.49856.5880.65381.75442.8539-2.38870.2508-1.6167-3.62551.9204-0.90941.18950.08270.5160.97540.25351.3554181.1503132.5909-74.8826
1047.0118-5.5162-5.84754.37914.66034.97030.5646-0.63880.0106-0.0725-0.1564-1.70650.06491.9459-0.41320.72430.05710.02670.72910.05020.8085186.3483128.2196-66.4125
1059.95360.2257-4.99196.79841.36734.1610.5211-0.20380.54080.554-0.09670.1461-0.4827-0.4061-0.36840.69090.12620.24280.77990.21960.5748175.6683126.9206-67.4412
1066.17177.18965.59469.42276.8955.2035-0.18571.45130.048-0.14631.2479-0.7094-1.01771.9142-1.01270.75-0.06990.16231.0878-0.03310.6726192.799125.7363-71.3197
1076.91425.0426-5.65999.2838-9.37759.6858-0.31271.754-0.6497-1.43580.08310.67981.7966-1.08590.21721.1195-0.2762-0.47052.0525-0.26251.2924251.4456113.251527.6445
1087.1672-4.3615.35488.6741-6.30685.5439-1.3844-2.51230.58383.53730.9152-1.2831-0.73270.30.48141.39920.0318-0.27142.2436-0.11140.8855250.7188100.208842.3165
1093.50084.4573-3.94087.4923-2.79378.8338-0.9225-1.3773-0.4511.48740.7481-0.7435-0.0713-0.05450.17511.405-0.33150.0651.6661-0.23191.1092245.965693.60937.6168
1100.4827-0.2167-0.25420.59980.11150.1341-0.5845-2.15771.06591.20.2818-0.5759-0.4472-0.37450.28831.1743-0.2109-0.29992.1146-0.16510.7834246.4673105.182529.4836
1116.4211-1.3872-2.16495.0429-3.17514.3530.0809-2.0662-0.21691.1012-0.1118-0.55260.08930.12280.05191.0634-0.1284-0.09671.4773-0.02990.5865249.231996.813629.2241
1126.8945-4.66584.55263.2336-3.05993.0149-0.6945-0.15890.32610.50380.5444-0.4294-0.43640.72270.14341.0988-0.2305-0.00931.1899-0.02510.6551240.54797.429518.2249
1132.7448-1.9043.65111.9128-2.45084.84180.19840.11370.1245-0.0915-0.00850.37090.6402-0.0653-0.1940.7308-0.16850.16750.51410.18240.7599107.804442.2253-19.6946
1140.16330.1066-0.06230.0832-0.03880.02340.4076-1.6488-0.41181.579-0.396-0.2494-0.40340.2424-0.03620.8342-0.1584-0.11350.85820.27110.5882105.483851.9204-14.5837
1153.17663.62293.14215.71885.7657.94-0.27990.41080.1704-0.94570.1843-0.6499-1.24621.39030.06360.6643-0.17960.11070.73060.39330.9469103.088652.6096-31.1052
1167.0807-5.4846-4.14.25393.29174.42550.4360.7652-1.1539-0.5593-0.68391.77561.0087-3.35310.2080.8494-0.0521-0.06691.2051-0.00710.920592.598648.3469-38.7924
1172.5469-4.4048-1.40829.41494.7673.81170.5567-1.11080.12931.7755-0.44670.0010.4139-0.321-0.14070.8445-0.46390.06981.28-0.42981.0531250.9704124.37242.289
1184.823-5.23145.37256.157-4.44799.9236-0.41360.3372-0.1351-0.68140.1205-1.4495-0.82480.94530.310.8937-0.36960.24940.8606-0.31331.1175247.5425129.63763.5894
1196.5324-5.731.69535.4904-3.56869.764-0.7122-0.10071.06391.2424-0.0224-0.7875-1.70260.48260.7011.0199-0.3527-0.13741.5714-0.65820.9925253.4454133.17659.7208
1203.76922.48142.80033.3843-0.63875.9602-0.1979-0.97981.43060.63790.51920.1984-0.8018-0.4278-0.31410.84570.1114-0.03361.272-0.32711.2167192.0735103.7013-0.9073
1216.6647-1.3585-4.70516.6152.09353.51950.3207-1.37110.41171.59480.2159-2.37160.45582.1466-0.41830.8270.0113-0.241.8975-0.49641.2456204.974295.56914.4174
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:920)
2X-RAY DIFFRACTION2chain 'A' and (resseq 921:1400)
3X-RAY DIFFRACTION3chain 'A' and (resseq 1401:1532)
4X-RAY DIFFRACTION4chain 'A' and (resseq 1533:1541)
5X-RAY DIFFRACTION5chain 'B' and (resseq 7:25)
6X-RAY DIFFRACTION6chain 'B' and (resseq 26:64)
7X-RAY DIFFRACTION7chain 'B' and (resseq 65:86)
8X-RAY DIFFRACTION8chain 'B' and (resseq 87:122)
9X-RAY DIFFRACTION9chain 'B' and (resseq 123:148)
10X-RAY DIFFRACTION10chain 'B' and (resseq 149:226)
11X-RAY DIFFRACTION11chain 'B' and (resseq 227:240)
12X-RAY DIFFRACTION12chain 'C' and (resseq 2:112)
13X-RAY DIFFRACTION13chain 'C' and (resseq 113:207)
14X-RAY DIFFRACTION14chain 'D' and (resseq 2:34)
15X-RAY DIFFRACTION15chain 'D' and (resseq 35:67)
16X-RAY DIFFRACTION16chain 'D' and (resseq 68:148)
17X-RAY DIFFRACTION17chain 'D' and (resseq 149:181)
18X-RAY DIFFRACTION18chain 'D' and (resseq 182:209)
19X-RAY DIFFRACTION19chain 'E' and (resseq 5:14)
20X-RAY DIFFRACTION20chain 'E' and (resseq 15:27)
21X-RAY DIFFRACTION21chain 'E' and (resseq 28:50)
22X-RAY DIFFRACTION22chain 'E' and (resseq 51:63)
23X-RAY DIFFRACTION23chain 'E' and (resseq 64:79)
24X-RAY DIFFRACTION24chain 'E' and (resseq 80:86)
25X-RAY DIFFRACTION25chain 'E' and (resseq 87:103)
26X-RAY DIFFRACTION26chain 'E' and (resseq 104:140)
27X-RAY DIFFRACTION27chain 'E' and (resseq 141:154)
28X-RAY DIFFRACTION28chain 'F' and (resseq 1:32)
29X-RAY DIFFRACTION29chain 'F' and (resseq 33:92)
30X-RAY DIFFRACTION30chain 'F' and (resseq 93:101)
31X-RAY DIFFRACTION31chain 'G' and (resseq 2:11)
32X-RAY DIFFRACTION32chain 'G' and (resseq 12:20)
33X-RAY DIFFRACTION33chain 'G' and (resseq 21:52)
34X-RAY DIFFRACTION34chain 'G' and (resseq 53:57)
35X-RAY DIFFRACTION35chain 'G' and (resseq 58:79)
36X-RAY DIFFRACTION36chain 'G' and (resseq 80:92)
37X-RAY DIFFRACTION37chain 'G' and (resseq 93:109)
38X-RAY DIFFRACTION38chain 'G' and (resseq 110:129)
39X-RAY DIFFRACTION39chain 'G' and (resseq 130:144)
40X-RAY DIFFRACTION40chain 'G' and (resseq 145:156)
41X-RAY DIFFRACTION41chain 'H' and (resseq 1:18)
42X-RAY DIFFRACTION42chain 'H' and (resseq 19:29)
43X-RAY DIFFRACTION43chain 'H' and (resseq 30:41)
44X-RAY DIFFRACTION44chain 'H' and (resseq 42:53)
45X-RAY DIFFRACTION45chain 'H' and (resseq 54:62)
46X-RAY DIFFRACTION46chain 'H' and (resseq 63:72)
47X-RAY DIFFRACTION47chain 'H' and (resseq 73:85)
48X-RAY DIFFRACTION48chain 'H' and (resseq 86:95)
49X-RAY DIFFRACTION49chain 'H' and (resseq 96:100)
50X-RAY DIFFRACTION50chain 'H' and (resseq 101:106)
51X-RAY DIFFRACTION51chain 'H' and (resseq 107:116)
52X-RAY DIFFRACTION52chain 'H' and (resseq 117:127)
53X-RAY DIFFRACTION53chain 'H' and (resseq 128:138)
54X-RAY DIFFRACTION54chain 'I' and (resseq 2:25)
55X-RAY DIFFRACTION55chain 'I' and (resseq 26:32)
56X-RAY DIFFRACTION56chain 'I' and (resseq 33:53)
57X-RAY DIFFRACTION57chain 'I' and (resseq 54:88)
58X-RAY DIFFRACTION58chain 'I' and (resseq 89:97)
59X-RAY DIFFRACTION59chain 'I' and (resseq 98:117)
60X-RAY DIFFRACTION60chain 'I' and (resseq 118:128)
61X-RAY DIFFRACTION61chain 'J' and (resseq 3:29)
62X-RAY DIFFRACTION62chain 'J' and (resseq 30:42)
63X-RAY DIFFRACTION63chain 'J' and (resseq 43:47)
64X-RAY DIFFRACTION64chain 'J' and (resseq 48:70)
65X-RAY DIFFRACTION65chain 'J' and (resseq 71:78)
66X-RAY DIFFRACTION66chain 'J' and (resseq 79:85)
67X-RAY DIFFRACTION67chain 'J' and (resseq 86:93)
68X-RAY DIFFRACTION68chain 'J' and (resseq 94:100)
69X-RAY DIFFRACTION69chain 'K' and (resseq 11:34)
70X-RAY DIFFRACTION70chain 'K' and (resseq 35:57)
71X-RAY DIFFRACTION71chain 'K' and (resseq 58:75)
72X-RAY DIFFRACTION72chain 'K' and (resseq 76:100)
73X-RAY DIFFRACTION73chain 'K' and (resseq 101:110)
74X-RAY DIFFRACTION74chain 'K' and (resseq 111:126)
75X-RAY DIFFRACTION75chain 'L' and (resseq 5:32)
76X-RAY DIFFRACTION76chain 'L' and (resseq 33:128)
77X-RAY DIFFRACTION77chain 'M' and (resseq 2:14)
78X-RAY DIFFRACTION78chain 'M' and (resseq 15:21)
79X-RAY DIFFRACTION79chain 'M' and (resseq 22:61)
80X-RAY DIFFRACTION80chain 'M' and (resseq 62:83)
81X-RAY DIFFRACTION81chain 'M' and (resseq 84:93)
82X-RAY DIFFRACTION82chain 'M' and (resseq 94:119)
83X-RAY DIFFRACTION83chain 'N' and (resseq 2:11)
84X-RAY DIFFRACTION84chain 'N' and (resseq 12:16)
85X-RAY DIFFRACTION85chain 'N' and (resseq 17:24)
86X-RAY DIFFRACTION86chain 'N' and (resseq 25:29)
87X-RAY DIFFRACTION87chain 'N' and (resseq 30:61)
88X-RAY DIFFRACTION88chain 'O' and (resseq 2:15)
89X-RAY DIFFRACTION89chain 'O' and (resseq 16:49)
90X-RAY DIFFRACTION90chain 'O' and (resseq 50:73)
91X-RAY DIFFRACTION91chain 'O' and (resseq 74:88)
92X-RAY DIFFRACTION92chain 'P' and (resseq 1:19)
93X-RAY DIFFRACTION93chain 'P' and (resseq 20:43)
94X-RAY DIFFRACTION94chain 'P' and (resseq 44:52)
95X-RAY DIFFRACTION95chain 'P' and (resseq 53:62)
96X-RAY DIFFRACTION96chain 'P' and (resseq 63:83)
97X-RAY DIFFRACTION97chain 'Q' and (resseq 2:17)
98X-RAY DIFFRACTION98chain 'Q' and (resseq 18:82)
99X-RAY DIFFRACTION99chain 'Q' and (resseq 83:100)
100X-RAY DIFFRACTION100chain 'R' and (resseq 19:23)
101X-RAY DIFFRACTION101chain 'R' and (resseq 24:28)
102X-RAY DIFFRACTION102chain 'R' and (resseq 29:36)
103X-RAY DIFFRACTION103chain 'R' and (resseq 37:43)
104X-RAY DIFFRACTION104chain 'R' and (resseq 44:52)
105X-RAY DIFFRACTION105chain 'R' and (resseq 53:76)
106X-RAY DIFFRACTION106chain 'R' and (resseq 77:88)
107X-RAY DIFFRACTION107chain 'S' and (resseq 2:12)
108X-RAY DIFFRACTION108chain 'S' and (resseq 13:25)
109X-RAY DIFFRACTION109chain 'S' and (resseq 26:35)
110X-RAY DIFFRACTION110chain 'S' and (resseq 36:40)
111X-RAY DIFFRACTION111chain 'S' and (resseq 41:70)
112X-RAY DIFFRACTION112chain 'S' and (resseq 71:81)
113X-RAY DIFFRACTION113chain 'T' and (resseq 8:66)
114X-RAY DIFFRACTION114chain 'T' and (resseq 67:75)
115X-RAY DIFFRACTION115chain 'T' and (resseq 76:91)
116X-RAY DIFFRACTION116chain 'T' and (resseq 92:106)
117X-RAY DIFFRACTION117chain 'U' and (resseq 2:8)
118X-RAY DIFFRACTION118chain 'U' and (resseq 9:15)
119X-RAY DIFFRACTION119chain 'U' and (resseq 16:25)
120X-RAY DIFFRACTION120chain 'a' and (resseq 1:6)
121X-RAY DIFFRACTION121chain 'b' and (resseq 30:40)

+
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

+
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