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- PDB-5wnu: 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: 5wnu
タイトルCrystal Structure of 30S ribosomal subunit from Thermus thermophilus
要素
  • (30S ribosomal protein ...) x 20
  • 16S Ribosomal RNA rRNA
  • RNA (5'-R(*AP*(A2M)P*A)-3')
  • RNA (5'-R(P*UP*(70U)P*UP*UP*(12A)P*A)-3')
キーワードRIBOSOME / smFRET / mRNA methylation / translation / decoding
機能・相同性
機能・相同性情報


ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding ...ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
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 S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, 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 domain superfamily / Ribosomal protein S16 / 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 / K Homology domain / K homology RNA-binding domain / Few Secondary Structures / Irregular / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / : / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / K homology domain superfamily, prokaryotic type / Ribosomal protein S5, N-terminal
類似検索 - ドメイン・相同性
Chem-B6M / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 ...Chem-B6M / : / : / RNA / 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 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
類似検索 - 構成要素
生物種Thermus thermophilus (バクテリア)
手法X線回折 / シンクロトロン / フーリエ合成 / 解像度: 3.4 Å
データ登録者DeMirci, H.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM51266 and GM099687 米国
引用ジャーナル: Nat. Struct. Mol. Biol. / 年: 2018
タイトル: 2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation.
著者: Choi, J. / Indrisiunaite, G. / DeMirci, H. / Ieong, K.W. / Wang, J. / Petrov, A. / Prabhakar, A. / Rechavi, G. / Dominissini, D. / He, C. / Ehrenberg, M. / Puglisi, J.D.
履歴
登録2017年8月1日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年2月21日Provider: repository / タイプ: Initial release
改定 1.12018年3月7日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
改定 1.22018年3月14日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32018年3月21日Group: Source and taxonomy / Structure summary
カテゴリ: entity / entity_name_com ...entity / entity_name_com / entity_src_nat / pdbx_entity_src_syn
Item: _entity.pdbx_description / _entity.src_method ..._entity.pdbx_description / _entity.src_method / _entity_name_com.entity_id / _pdbx_entity_src_syn.entity_id / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific
改定 1.42020年1月1日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.52020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.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: 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'-R(*AP*(A2M)P*A)-3')
b: RNA (5'-R(P*UP*(70U)P*UP*UP*(12A)P*A)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)778,182300
ポリマ－770,45123
非ポリマー7,731277
水4,089227
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: mass spectrometry
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)400.000, 400.000, 173.000
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 Aab

#1: RNA鎖 16S Ribosomal RNA rRNA


分子量: 494170.781 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: GenBank: 55771382
#22: RNA鎖 RNA (5'-R(*AP*(A2M)P*A)-3')


分子量: 956.687 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579
#23: RNA鎖 RNA (5'-R(P*UP*(70U)P*UP*UP*(12A)P*A)-3')


分子量: 2117.451 Da / 分子数: 1 / 由来タイプ: 合成
由来: (合成) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)

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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) (バクテリア)
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) (バクテリア)
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) (バクテリア)
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) (バクテリア)
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) (バクテリア)
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) (バクテリア)
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) (バクテリア)
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) (バクテリア)
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) (バクテリア)
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) (バクテリア)
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) (バクテリア)
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) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P80377
#14: タンパク質 30S ribosomal protein S14 type Z


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) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P0DOY6
#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) (バクテリア)
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) (バクテリア)
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) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P0DOY7
#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) (バクテリア)
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) (バクテリア)
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) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P80380
#21: タンパク質・ペプチド 30S ribosomal protein Thx / 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)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q5SIH3

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非ポリマー , 5種, 504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-K / POTASSIUM ION / カリウムカチオン


分子量: 39.098 Da / 分子数: 22 / 由来タイプ: 合成 / 式: K
#26: 化合物 ChemComp-B6M / (1R,2S,3S,4R,6R)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-alpha-L-altropyranosyl)-beta-L-arabinofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-allopyranoside


分子量: 615.628 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C23H45N5O14
#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


分子量: 18.015 Da / 分子数: 227 / 由来タイプ: 合成 / 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: 4.49 Å3/Da / 溶媒含有率: 72.61 %
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: 2.92→39.801 Å / Num. obs: 295340 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / 冗長度: 76.135 % / Biso Wilson estimate: 161.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.716 / Rrim(I) all: 0.72 / Χ2: 0.961 / Net I/σ(I): 8.25 / Num. measured all: 22485694 / Scaling rejects: 20962
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Num. measured obsNum. possibleNum. unique obs% possible allMean I/σ(I) obsCC1/2Rmerge(I) obsRrim(I) all
2.92-2.9939.52714882220971808981.9
2.99-3.0750.5321031512215332041394.8
3.07-3.1674.4141549070209202081799.5
3.16-3.2682.2251672617203772034299.80.01
3.26-3.3783.3081640174197161968899.90.180.117
3.37-3.4981.4971554065190911906999.90.310.199
3.49-3.6276.9211413801184401838099.70.470.312
3.62-3.7785.541520990177961778199.91.060.4936.3326.369
3.77-3.9385.0151447469170391702699.91.710.6574.0314.055
3.93-4.1383.337135972916321163161002.520.7982.8982.915
4.13-4.3580.4631250321155471553999.93.740.8862.0312.043
4.35-4.6179.0651160043147061467299.85.560.9361.3811.39
4.61-4.9384.39117217113896138901008.580.9740.9520.958
4.93-5.3382.971072217129341292399.911.960.9870.6860.69
5.33-5.8378.105927024119091186999.715.980.9920.5050.509
5.83-6.5283.161901294108401083810021.30.9960.3760.378
6.52-7.5382.3897934939631963110033.980.9990.2210.222
7.53-9.2273.8876000338169812199.4480.9990.1340.135
9.22-13.0574.4014771316413641310074.710.0720.073
13.05-39.80164.622276583726352394.691.4410.0440.045

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解析

ソフトウェア
名称バージョン分類
PHENIX精密化
XSCALEデータスケーリング
PDB_EXTRACT3.22データ抽出
XDSデータ削減
PHENIX位相決定
精密化構造決定の手法: フーリエ合成 / 解像度: 3.4→39.801 Å / SU ML: 0.55 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 27.68 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2311 1250 0.68 %
Rwork0.1872 183594 -
obs0.1875 184844 96.83 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 461.55 Å2 / Biso mean: 176.7688 Å2 / Biso min: 76.81 Å2
精密化ステップサイクル: final / 解像度: 3.4→39.801 Å
タンパク質核酸リガンド溶媒全体
原子数18910 32918 629 0 52457
Biso mean--176.98 --
残基数----3910
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00156311
X-RAY DIFFRACTIONf_angle_d0.4483534
X-RAY DIFFRACTIONf_chiral_restr0.02810388
X-RAY DIFFRACTIONf_plane_restr0.0034902
X-RAY DIFFRACTIONf_dihedral_angle_d13.3130269
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.53610.38221130.3553161771629078
3.5361-3.69690.34491310.3292197371986895
3.6969-3.89170.3031420.26982089521037100
3.8917-4.13520.31781420.24342088521027100
4.1352-4.45410.25681440.20772094821092100
4.4541-4.90170.2261420.16942097821120100
4.9017-5.60920.211450.15292108621231100
5.6092-7.06060.22631440.17032119021334100
7.0606-39.80420.19341470.1674216982184599
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)
10.49250.2189-0.21680.5969-0.11840.478-0.0006-0.01680.00550.20940.09120.16590.11150.0549-0.08771.17910.16670.07341.1095-0.04111.5028143.28283.168-12.669
21.1893-0.31890.05110.5361-0.08970.51740.0319-0.82170.42510.37930.0283-0.0952-0.22560.1226-0.04541.2804-0.24040.1191.9722-0.6211.6223221.477128.9029.458
32.65511.3802-1.06520.7061-0.70190.3135-0.3203-0.1136-0.6847-0.21670.245-0.51990.27110.12350.07621.47370.17940.0111.4247-0.07981.6874162.74968.975-25.958
41.77940.94220.35544.0726-2.67159.58161.93872.55993.761-2.9948-3.0975-6.6791-0.95615.36151.19842.1147-0.35330.47474.41290.27092.6827202.991111.91-33.372
58.6629-5.15944.24373.5541-1.08776.0162-0.1490.68191.1235-2.16950.4685-1.1168-0.40911.6295-0.29691.4075-0.24760.41950.72080.16081.6221156.285155.576-35.86
67.4701-1.4527-1.3027.58753.7556.65160.5873-0.34461.0979-1.27550.2470.0602-0.571-1.1346-0.85531.4050.19070.22561.09830.02882.4628149.012155.592-27.742
73.3838-0.7669-1.26563.6678-3.91655.81130.33480.11472.95680.5747-0.0363-0.2182-2.40562.4057-0.341.5542-0.38210.28691.4916-0.05662.0782166.238162.118-19.339
85.12185.15691.48167.5951-2.27556.48950.5091-0.92720.86240.7509-0.18191.5625-1.1980.1149-0.34191.20820.01340.46431.2852-0.57241.9904173.248157.061-6.981
98.79447.15076.18828.93076.41828.10180.18081.217-0.57521.88421.8695-0.92340.03742.5881-2.01032.3978-0.36530.31451.5958-0.99672.9189189.273162.274-5.127
103.66190.41272.42872.743-2.91375.51320.15110.14870.2774-0.66760.4507-0.1883-0.71840.2416-0.57111.85120.01410.72920.8633-0.30352.3451159.345156.035-18.684
111.68912.7711-1.35056.3734-2.53692.61430.53360.09091.1334-0.25310.3360.7357-1.7879-0.2942-0.84513.06140.08460.86231.02150.67213.6613162.645174.087-23.619
124.1113-0.1634-0.15151.5429-1.20981.133-0.045-1.08560.6250.80870.2536-0.0089-0.6204-0.0408-0.21211.8484-0.0910.08942.691-1.01361.6073204.077141.25233.5
131.8008-2.76071.44529.2029-0.45231.7426-0.1796-1.23650.14510.71740.20781.27640.0478-1.1301-0.04341.1647-0.04410.37253.1195-0.70321.8663188.845132.87417.462
148.7702-3.9417-0.73035.5776-3.93614.8255-0.21290.0991-0.332-1.15091.7371.25090.64250.1893-1.59021.7196-0.23520.15311.1662-0.21391.6412154.629110.52437.45
157.06612.42210.00843.2078-2.43262.47260.1578-1.43211.26680.4579-0.15860.0651-0.67670.78760.20791.86030.02080.12521.3691-0.20771.3195160.676112.32925.119
164.88671.12991.40376.4992-6.22387.27640.3195-0.2560.07041.0884-0.373-0.17640.3695-0.24620.07471.65180.07240.37051.0171-0.28811.2343136.331103.18730.857
176.66310.9214-0.88175.2719-5.21915.19170.5441-2.40671.3622.92120.32991.3388-2.0337-0.1307-0.85952.20480.12020.35741.6037-0.34221.2801132.722109.35547.545
184.77861.3552-4.30257.2903-1.9323.92622.47930.74051.8418-0.5634-0.9263-0.1691-3.6659-0.9827-1.55771.76160.24770.02921.32570.01581.378139.786113.55823.358
192.02131.99852.04094.73764.75214.77730.4648-3.68413.78962.13071.3549-1.59940.64821.5196-1.74211.3154-0.10790.09411.4975-0.46411.4806161.309126.3688.114
204.01952.8854-4.41152.4182-3.28414.8891-0.95940.0551-1.59670.00290.2808-1.2278-0.81920.86020.70831.2016-0.17920.23552.0237-0.70511.873183.295121.987-2.579
213.97930.2254-5.57732.9547-1.09248.0014-0.4235-1.96513.2826-0.26141.41540.0696-0.44221.4036-0.98261.2055-0.38430.08031.4497-0.82771.9361161.269129.1284.432
224.4136-5.3613.07017.601-1.54797.5569-0.88020.66853.05180.92450.1266-0.2706-1.28060.66630.78311.6868-0.84250.56971.3552-0.34612.0344167.015133.0345.209
231.62252.2994-2.91323.3839-4.10445.26652.0915-1.4695.02991.1068-1.43964.0107-0.3894-0.6408-0.78521.26080.12720.36491.2391-0.41142.1782144.543128.8540.419
244.19823.0752-4.81036.7057-5.71436.5845-0.7394.0818-2.2166-0.9656-0.01911.68591.3033-1.03340.7841.01590.20810.30221.5439-0.44852.0305151.924119.586-10.983
255.404-5.8268-5.66676.83776.36026.0456-1.5243-0.6043-1.82060.64490.04461.28550.4988-0.26411.49511.58320.35070.3511.0707-0.29191.6502144.963116.2130.884
267.16830.11924.81647.03744.12265.87530.2043-0.3772-0.367-0.0344-0.14770.17250.47060.8696-0.0810.9892-0.19140.34311.1296-0.22641.2355152.613120.353-0.55
275.0815-5.23494.95995.4112-5.13354.8788-0.63290.18641.95811.3919-0.1976-0.656-2.32-1.59080.80331.28230.36710.17351.2273-0.41642.1453135.852133.707-9.388
289.86833.0603-5.89752.24470.31947.647-0.88211.88360.6286-1.16530.38490.6521.09860.06490.50561.60650.1404-0.03142.03270.06921.1696173.493114.805-93.667
299.8261-0.78736.01769.18691.7827.81860.8931.4478-0.4648-0.9898-0.4081-0.15270.16190.1231-0.42571.32470.13130.13231.6583-0.02431.1331174.357115.67-87.307
303.78844.64814.78915.72915.89856.048-1.4748-0.48431.7015-2.10851.06683.1622-2.4706-2.25280.46631.8770.237-0.21912.0620.77792.2032164.957131.429-73.583
315.83662.694-5.09767.8259-5.10265.6031.7283-1.18938.20640.3757-1.70173.8093-0.9508-1.384-0.16711.1506-0.03570.30441.6467-0.41932.9743216.492142.526-23.222
323.5034.2493-4.07885.39-5.08284.8262-1.20470.6746-2.99210.49831.0388-1.19482.392-0.92160.23131.7553-0.22450.19081.20450.02312.8947238.42151.984-24.769
339.3616-4.333.11983.083-3.92586.937-1.6098-0.11540.15191.03240.706-1.2338-0.96310.59890.78091.3052-0.16260.12711.4424-0.66521.8466244.21142.629-22.541
342.3128-2.67520.97873.7825-3.16866.368-0.47071.00331.5996-0.93560.73641.6886-0.56250.4786-0.21152.1396-1.36250.43921.822-0.30372.4224252.572146.853-36.787
353.94986.0695.14099.69836.89917.5686-0.23881.541.5004-0.81340.07670.4422-0.04730.78030.17841.25560.2870.11761.53030.36241.2643232.265136.363-37.542
365.15266.61065.55128.46547.1215.97121.38710.0886-0.52671.7582-0.6888-0.59723.02221.5067-0.64722.02110.2685-0.43591.99070.13631.4919218.692124.373-38.83
376.3454-5.24136.29144.3917-5.70469.70720.1202-0.5995-1.2120.36910.59061.22440.0539-1.665-0.74561.1536-0.29550.4771.3172-0.05952.2825234.019135.261-30.704
385.0647-5.21085.44178.4921-3.94026.69320.44282.62160.8485-0.62340.069-0.77010.58744.1414-0.22841.0497-0.19090.67352.0835-0.05541.9219249.688134.042-30.287
397.46173.84725.22552.61262.62514.7273-1.06525.8451-4.9192-2.3411.7222-2.87292.86181.548-0.63561.83040.14740.10471.7989-0.5861.6005236.724128.128-40.342
404.4613-4.6978-5.16334.95625.44836.00370.2734-2.69715.5353.07140.51491.9052-2.268-0.6678-0.77292.0380.31720.17711.5314-0.422.0375218.744125.182-44.504
417.37311.8031-1.42522.1817-2.18372.2010.1954-0.1939-1.0075-1.2659-0.0551-0.48021.3671.7624-0.16271.05570.31950.31081.0857-0.07971.3552139.425122.4-30.821
429.00146.69446.92495.01195.17825.33760.25530.6186-0.0049-0.5753-0.4011-0.7451-0.92740.27080.18861.07150.08160.26161.10980.11591.4562138.49132.076-31.885
438.03275.07794.13993.26172.55032.2844-0.9706-0.03850.7118-0.0821-0.11742.538-1.0234-1.74111.13311.14090.21340.07471.2450.33931.7677125.829125.473-27.72
443.69580.79164.49384.83982.09875.7571-0.8144-0.18980.37-0.73380.35842.6599-3.1788-1.44880.45231.59030.0763-0.03291.01830.23922.1386129.745132.865-30.037
455.29114.87565.22994.51684.81145.1712-0.08931.37710.7953-0.24190.8427-1.7309-1.27760.075-0.69731.10860.14410.12061.16010.19641.9253132.845131.65-39.053
466.49517.54623.23482.01075.40459.1764-0.4569-2.56863.68840.5975-0.41691.9687-1.2915-0.90720.87991.56070.12360.4671.0765-0.42232.462144.647139.809-17.101
472.47652.69484.12553.03244.59266.91720.2751-1.05391.3948-0.3827-0.65630.7605-1.0045-0.32850.3161.21630.27870.13091.0826-0.08791.7307142.646129.141-18.853
484.53844.607-6.41134.6727-6.5249.4319-1.55270.0129-0.26420.42291.0138-0.39320.25520.11950.47851.17770.14260.0011.4088-0.01541.1699133.256108.601-24.604
491.8754-2.11831.29988.93333.22174.2594-1.939-1.7471-4.25562.2441.31922.56992.50841.28230.55441.1460.62690.59411.59670.48942.6412124.707109.512-12.473
503.28322.92140.05743.73671.78132.7137-0.1777-1.8874-5.23610.59130.0138-4.94421.75351.40320.16641.43360.03760.04411.3950.06742.2953133.375118.891-8.69
518.06343.73545.37656.76764.48094.3715-0.7727-1.4155-0.33610.7828-1.00540.40161.9180.33151.68361.2450.03210.42261.41110.32011.6141125.495118.427-19.148
527.72997.9304-4.28819.92-5.84073.5425-0.63620.00912.58880.8928-0.1795-1.0661-1.4782-2.28340.75420.90070.22470.32981.4765-0.12362.7343121.736119.661-15.622
532.28762.69463.25113.26844.27297.91260.9919-0.806-4.07231.6574-0.128-2.14950.6378-0.1592-0.99221.10480.13510.0321.0280.40291.6269130.484116.902-19.286
549.5779-6.6946-5.80717.93270.81486.79030.4489-0.86270.5193-0.3247-0.0311.9564-0.39450.4515-0.52011.5319-0.41970.41761.6622-0.82243.4019238.278166.353-4.811
556.68332.39795.54632.98430.78725.2822-0.11150.5799-0.53050.5332-0.5023-2.0089-0.73462.61410.51580.8619-0.5931-0.61232.0309-0.52862.5903248.871161.511-3.966
561.571-3.29611.4336.8832-3.19512.88750.09530.02991.6338-0.1467-1.2802-1.31620.22520.86151.15291.1262-0.32950.32581.5729-0.03752.0744243.738158.207-13.646
574.1687-3.90730.34434.8972-3.24656.62050.509-0.25191.59310.9563-0.48140.635-1.36191.8046-0.05571.3426-0.4954-0.09721.6176-0.65083.2432238.531164.317-8.737
586.22484.97665.94319.7957.39676.8961-0.54451.11430.3427-0.63340.8903-1.2665-1.20721.2322-0.35491.3898-0.3704-0.16751.5064-0.38183.3035228.353171.981-17.565
594.77381.99860.14578.3061-2.44851.0552-0.1781-0.19550.98960.54830.4151-0.7281-0.27210.1536-0.29771.4393-0.35050.21822.1799-0.90712.0518224.95147.265-6.682
609.7637-6.57091.14057.1504-5.60059.3689-0.45770.324-1.0658-1.31941.0404-2.98941.3952-0.9049-0.61271.7115-0.39470.08762.0889-0.77411.944221.524124.069-6.978
619.95056.54036.60334.32514.67486.7258-0.93570.68960.72131.98130.76121.621-0.98780.62610.23781.98840.1189-0.16122.1522-0.96422.6493220.598162.45526.811
623.8173-4.89022.91446.4878-3.14563.59130.7929-0.52490.99330.7672-0.88540.8084-2.1867-0.4580.17632.3821-0.22450.35272.1652-1.57592.9028226.328165.80623.047
632.50362.95023.3863.81744.28054.824-0.02242.51520.69270.25932.187-0.2451-1.82122.9413-2.08082.1578-0.33890.84853.1667-0.62412.1005223.937142.04917.107
645.622.0343-3.59273.2052-4.8177.3407-1.11170.1445-0.5651-3.82012.2935-3.2155-1.3081-0.2251-1.14461.5128-0.08210.48212.2386-0.9371.9272216.915135.31113.26
656.5115-6.0863-6.28736.23245.27836.73310.8376-2.13491.95112.251-2.57521.6922-2.684-0.12641.86362.9374-0.8679-0.95892.7079-1.40684.3105229.649169.13730.157
668.0999-6.1951-2.76735.9512-0.49666.5702-1.5041-3.62693.41082.15642.1373-1.5185-3.2816-0.2921-0.75922.84790.86820.78012.539-1.21053.7691222.701171.92239.275
670.43360.3483-0.72221.0248-1.29011.88292.2121-1.1974-3.210.56531.3299-0.78810.32930.7921-3.38412.30710.2881-0.61065.0549-1.44222.8191214.939160.1335.18
684.36595.66734.84857.52946.21975.4101-1.5993.0199-4.24960.68652.4513-2.83590.78964.3825-0.85342.22271.0945-0.55913.612-1.1442.4184226.658156.52232.947
694.7184-1.82843.32239.6483-5.57474.4407-0.32521.2554-0.959-0.25190.699-0.1143-0.0338-1.7722-0.31411.157-0.16460.21771.4999-0.23961.5696212.322118.571-69.086
707.45240.93684.55562.2526-0.49863.6140.89370.8115-0.1957-0.81690.7657-1.0093-0.42553.9459-1.56581.22120.01780.25361.5983-0.20041.1552216.56114.777-62.508
714.61913.8928-4.73333.5162-3.98294.85620.11780.19111.26690.51350.1723-2.3336-0.56691.7528-0.31260.8063-0.10560.01071.263-0.02741.7545220.537121.99-64.407
724.42184.3985-0.06644.4174-0.07862.0172-0.3945-0.83982.2705-0.426-0.19740.82830.1644-0.69240.64781.24680.0245-0.04441.3928-0.13431.4698210.628125.853-64.644
735.5554-2.58612.49287.95544.3835.6553-0.44410.52591.2288-0.8524-1.5234-1.7404-1.3335-0.13661.91351.3064-0.1983-0.02830.9730.45771.1795210.221129.665-69.636
745.58020.50281.82428.8926-8.0849.0769-0.56220.4986-1.0551-0.1837-0.2269-0.52480.539-0.19610.80321.44820.13210.1981.3839-0.31771.983192.948110.197-57.653
755.0225-5.47126.99996.3156-7.85429.880.0540.34940.3963-0.14460.0473-0.41120.44230.2292-0.09540.98520.07210.01211.2561-0.05941.248152.66788.782-13.986
765.2871-0.6762-4.61744.44763.68136.7521-0.33330.2151-0.130.74940.3078-0.61621.03210.74320.02981.25950.3213-0.21851.4620.05261.8581173.77778.4639.679
773.81620.30571.94286.4049-4.74449.6291-1.78270.3707-2.9473-2.39561.63664.23922.2141-1.1338-0.0141.5252-0.37860.21881.7768-0.52212.9444272.707115.112-8.287
788.8897-7.03964.53116.8295-5.29094.6098-0.55230.08740.90380.27520.62240.58990.16771.2769-0.05971.29310.3873-0.242.0072-0.371.8988267.226119.613-5.151
794.63066.3256-5.70478.9472-6.82059.74250.3143-0.919-0.2650.6416-1.1883-1.6936-0.81381.19720.80461.0547-0.1142-0.3121.7234-0.17862.1029274.399121.153-0.95
809.50286.2863-5.93124.1762-3.92943.7127-0.2048-1.58830.46151.3023-0.3774-1.20820.34791.98860.48911.5425-0.0143-0.15931.7727-0.18481.3539263.515103.6899.27
815.534-4.46594.55078.2451-3.59273.73540.00091.3376-1.636-0.0315-0.49771.7047-0.1188-2.34390.40181.00740.03690.08552.6203-0.38281.9621247.90398.20113.786
823.6145-0.72250.16259.48643.32259.446-0.1941-1.3399-0.12050.1006-0.10341.6419-0.130.65340.29651.2199-0.16120.25092.2205-0.11671.8215239.078102.9282.381
833.53514.6483.52266.73785.47844.64710.1284-0.3510.50682.2730.74670.20510.261-0.7293-0.96471.58960.43670.0682.6782-0.61281.4453218.544117.03533.719
842.00021.9994-7.97888.17835.79675.5382-1.4958-10.4415.40285.91496.5194-5.06623.22364.723-5.07623.0667-0.9913-0.3813.9762-0.41411.941230.433118.84139.355
859.9104-7.32116.87889.777-6.9518.998-1.12180.88871.32871.13670.0867-1.2837-0.34530.02140.97611.3629-0.44680.15132.3295-0.68582.0905226.869121.10430.268
864.3677-3.9910.67284.37010.74282.6504-0.0910.28220.96683.50221.614-2.84312.64163.4117-1.57631.7295-0.0355-0.48672.4007-0.60361.7102214.036124.76726.549
878.8251-1.66524.1334.8631-3.07945.6034-0.5575-1.68771.47640.1943-0.6452-0.33840.9665-1.78051.16261.2589-0.18310.16752.2099-0.80091.6941215.378134.32219.939
884.24023.8205-2.68183.5511-2.2032.3032-0.61275.59440.9869-2.89290.4019-0.19-2.3268-0.37460.24811.94690.31720.15192.53170.25121.3435140.866110.939-74.286
893.6954-3.8282-2.00394.04372.59678.0361-0.1071.2670.1876-0.94410.68810.3663-0.355-0.0197-0.48871.3428-0.0799-0.07181.2890.2611.1377144.394104.223-67
904.9642-2.3517-6.02398.23512.23087.35810.3033-2.723-0.32480.21470.20930.40410.62561.2234-0.49191.1326-0.0754-0.30581.45390.09171.1819143.059101.537-56.81
916.7662.0856-5.79973.6391-0.09616.56640.34051.2012-4.9932-1.0448-0.55821.1242.5244-3.06850.11051.2697-0.0947-0.70061.5352-0.21752.3241130.63997.598-64.508
926.73971.68776.86585.8349-1.66889.3810.1523-0.79210.06271.3859-0.12330.6679-0.56710.602-0.02181.86830.09590.48091.2564-0.07081.5339117.50776.515.164
935.66590.55662.95585.67373.22477.36090.1622-0.03262.0648-0.2054-0.06380.2103-0.29180.2791-0.13881.0865-0.01960.38650.9274-0.07881.7696114.95377.0510.608
944.38495.73223.50247.48934.45244.2666-0.4006-0.82172.4116-0.7432-0.93930.9474-2.2151-0.97751.28452.19040.36120.92891.06260.0782.3003109.71486.23420.75
954.254.75014.5375.35335.10434.8677-0.7741-0.00322.3069-2.3992-0.15040.5443-2.7702-1.39710.89631.66050.48620.34541.48210.71712.7929100.65179.2455.818
964.902-5.7799-1.23447.84832.66369.1366-0.2684-1.0553-3.02492.3307-0.47742.26210.6633-0.32530.79471.7542-0.2210.65610.96620.12872.1336101.08774.70616.603
978.43324.3484-3.25929.8442.41135.2747-0.01730.59620.5616-0.95650.6296-0.3434-0.2177-0.7766-0.65291.12630.0545-0.06311.2950.41461.5142119.54680.686-38.423
984.70771.59816.23665.35664.50349.3920.4888-0.3588-0.9976-0.04310.08020.28290.6529-0.473-0.55280.7311-0.07110.04941.0540.20111.213121.57584.495-35.597
996.2753-5.83916.4175.4238-5.96486.5219-0.05881.55050.2410.0055-0.3103-0.35770.02050.68320.34171.5057-0.28490.08051.5332-0.04741.4093137.685.256-44.604
1001.99990.5015-4.24153.10352.32565.05061.0877-2.46215.39513.5619-0.4198-1.182-2.33710.2134-0.47343.1115-0.34690.28530.8962-0.28752.0394180.05139.982-63.975
1013.4044-3.30890.79676.89112.52093.1488-0.9247-1.43410.5232-2.19950.81830.2878-1.4210.26680.09182.89970.05450.80371.6092-0.0732.5829174.389141.103-71.407
1027.0437-5.0958-5.36329.69593.57054.0880.0624-0.0454-0.1264-0.3977-1.195-1.80020.13810.60931.11870.94210.14230.112.05270.14721.8972171.852129.139-76.773
1033.6273.87162.0354.42763.01683.5433-0.17382.00852.5579-2.18440.94261.1242-4.16630.1396-0.8941.44550.05680.63571.21840.70211.5542180.698133.01-74.467
1046.742-4.8661-3.96334.951.2474.78631.3447-1.30921.20931.11240.2509-4.138-1.54883.9289-1.50021.0467-0.021-0.16311.8777-0.43851.4772185.969128.55-66.103
1055.0486-5.1363-5.02355.22955.12294.99971.3659-0.47340.97410.73530.7905-0.3238-0.6986-0.7461-1.99381.3255-0.06080.30331.39150.14111.1162175.3126.99-66.985
1069.68175.04645.02729.26263.05057.88750.04770.5409-0.88420.3660.1514-0.9875-0.71320.3768-0.23081.47040.08340.09351.59730.03771.4441192.508126.09-70.866
1079.75834.1881-6.32116.8164-5.96396.2801-1.61042.27630.7269-1.85570.64541.23212.1045-2.82040.99131.66640.2367-0.11573.2618-0.59312.0362250.821112.26827.738
1089.3254-4.21313.45168.7181-1.74045.9661-2.1481-4.001-0.17654.38351.77781.1322-1.377-3.48040.35081.71920.3604-0.08483.6922-0.21670.9208249.68198.93342.352
1099.5842-3.80931.27533.4314-4.15237.0966-1.38070.72861.40041.4158-0.084-3.6012-0.05491.10681.46971.0935-0.3239-0.36322.6318-0.03091.8757244.99192.29337.403
1101.837-3.4124-4.22069.15888.35339.8033-0.1223-4.68620.38370.8744-0.37740.5433-0.6269-2.72630.54681.32950.5314-0.29114.1067-0.15321.1985245.702104.13829.577
1116.2192-0.33880.95049.3436-3.99664.47460.0201-0.6508-0.92330.057-0.1338-1.7973-0.6469-0.47330.11041.19650.05910.00182.1882-0.16871.5003248.48895.51629.184
1125.7066-1.1645.48556.02970.35095.6286-0.4693-0.2629-0.0174-0.03330.0765-1.33860.21620.35550.36021.8863-0.11360.0352.56320.2232.0026239.98396.45418.056
1137.5069-2.31316.82971.9676-2.15445.710.6116-0.3004-0.3077-0.00160.17480.40320.5258-0.0935-0.80471.2588-0.10750.28060.84390.21121.4318107.38541.873-20.077
1146.8116-3.65065.12334.3123-0.82075.42061.58473.2361.2477-0.8633-0.42871.50620.23-1.5062-1.07561.01850.05730.09382.1670.40941.2605105.14451.444-15.101
1155.07824.22925.29094.34714.26286.0078-0.73411.65570.27190.6299-0.24540.8889-2.76483.41171.00921.2272-0.3627-0.00461.54160.68322.2032102.63652.382-31.595
1166.2845-4.9835-3.47374.13923.78137.3093-0.674-0.6957-1.2478-1.4333-2.15233.36310.7683-3.42552.42721.1192-0.3642-0.26141.6623-0.24922.3292.16547.998-39.288
1176.2881-4.95687.37462.0035-7.65359.1429-1.5677-4.8428-1.35052.95142.38882.0168-1.4673-1.6432-0.99421.28290.01840.34122.5598-1.08952.4884250.09123.8382.792
1186.86633.86595.30243.65543.02534.0946-0.3866-0.80272.6293-1.74870.26190.9095-0.64690.14040.16181.26970.0122-0.06681.0363-0.48562.373246.546129.0354.129
1194.6874-4.6013-4.71234.5344.63224.7525-1.0958-4.81352.40153.88861.1714-1.9148-1.59741.936-0.08282.0907-0.1155-0.25152.7193-0.64211.7652252.792132.44210.268
1207.6885-8.1312-7.51022.00047.27537.5869-1.0312-4.91482.71641.89024.4692-4.38490.47894.7095-3.40034.7094-1.5061-2.03954.31460.03273.3957194.10398.084-3.51
1215.36931.3943-0.08660.49020.72835.79072.2826-3.06750.74440.5539-0.4472-0.86861.32190.7281-1.5854.6008-2.88190.1287.0456-0.09462.5601201.16497.4433.06
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 920
2X-RAY DIFFRACTION2A921 - 1400
3X-RAY DIFFRACTION3A1401 - 1532
4X-RAY DIFFRACTION4A1533 - 1541
5X-RAY DIFFRACTION5B7 - 25
6X-RAY DIFFRACTION6B26 - 64
7X-RAY DIFFRACTION7B65 - 86
8X-RAY DIFFRACTION8B87 - 122
9X-RAY DIFFRACTION9B123 - 148
10X-RAY DIFFRACTION10B149 - 226
11X-RAY DIFFRACTION11B227 - 240
12X-RAY DIFFRACTION12C2 - 112
13X-RAY DIFFRACTION13C113 - 207
14X-RAY DIFFRACTION14D2 - 34
15X-RAY DIFFRACTION15D35 - 67
16X-RAY DIFFRACTION16D68 - 148
17X-RAY DIFFRACTION17D149 - 181
18X-RAY DIFFRACTION18D182 - 209
19X-RAY DIFFRACTION19E5 - 14
20X-RAY DIFFRACTION20E15 - 27
21X-RAY DIFFRACTION21E28 - 50
22X-RAY DIFFRACTION22E51 - 63
23X-RAY DIFFRACTION23E64 - 79
24X-RAY DIFFRACTION24E80 - 86
25X-RAY DIFFRACTION25E87 - 103
26X-RAY DIFFRACTION26E104 - 140
27X-RAY DIFFRACTION27E141 - 154
28X-RAY DIFFRACTION28F1 - 32
29X-RAY DIFFRACTION29F33 - 92
30X-RAY DIFFRACTION30F93 - 101
31X-RAY DIFFRACTION31G2 - 11
32X-RAY DIFFRACTION32G12 - 20
33X-RAY DIFFRACTION33G21 - 52
34X-RAY DIFFRACTION34G53 - 57
35X-RAY DIFFRACTION35G58 - 79
36X-RAY DIFFRACTION36G80 - 92
37X-RAY DIFFRACTION37G93 - 109
38X-RAY DIFFRACTION38G110 - 129
39X-RAY DIFFRACTION39G130 - 144
40X-RAY DIFFRACTION40G145 - 156
41X-RAY DIFFRACTION41H1 - 18
42X-RAY DIFFRACTION42H19 - 29
43X-RAY DIFFRACTION43H30 - 41
44X-RAY DIFFRACTION44H42 - 53
45X-RAY DIFFRACTION45H54 - 62
46X-RAY DIFFRACTION46H63 - 72
47X-RAY DIFFRACTION47H73 - 85
48X-RAY DIFFRACTION48H86 - 95
49X-RAY DIFFRACTION49H96 - 100
50X-RAY DIFFRACTION50H101 - 106
51X-RAY DIFFRACTION51H107 - 116
52X-RAY DIFFRACTION52H117 - 127
53X-RAY DIFFRACTION53H128 - 138
54X-RAY DIFFRACTION54I2 - 25
55X-RAY DIFFRACTION55I26 - 32
56X-RAY DIFFRACTION56I33 - 53
57X-RAY DIFFRACTION57I54 - 88
58X-RAY DIFFRACTION58I89 - 97
59X-RAY DIFFRACTION59I98 - 117
60X-RAY DIFFRACTION60I118 - 128
61X-RAY DIFFRACTION61J3 - 29
62X-RAY DIFFRACTION62J30 - 42
63X-RAY DIFFRACTION63J43 - 47
64X-RAY DIFFRACTION64J48 - 70
65X-RAY DIFFRACTION65J71 - 78
66X-RAY DIFFRACTION66J79 - 85
67X-RAY DIFFRACTION67J86 - 93
68X-RAY DIFFRACTION68J94 - 100
69X-RAY DIFFRACTION69K11 - 34
70X-RAY DIFFRACTION70K35 - 57
71X-RAY DIFFRACTION71K58 - 75
72X-RAY DIFFRACTION72K76 - 100
73X-RAY DIFFRACTION73K101 - 110
74X-RAY DIFFRACTION74K111 - 126
75X-RAY DIFFRACTION75L5 - 32
76X-RAY DIFFRACTION76L33 - 128
77X-RAY DIFFRACTION77M2 - 14
78X-RAY DIFFRACTION78M15 - 21
79X-RAY DIFFRACTION79M22 - 61
80X-RAY DIFFRACTION80M62 - 83
81X-RAY DIFFRACTION81M84 - 93
82X-RAY DIFFRACTION82M94 - 119
83X-RAY DIFFRACTION83N2 - 11
84X-RAY DIFFRACTION84N12 - 16
85X-RAY DIFFRACTION85N17 - 24
86X-RAY DIFFRACTION86N25 - 29
87X-RAY DIFFRACTION87N30 - 61
88X-RAY DIFFRACTION88O2 - 15
89X-RAY DIFFRACTION89O16 - 49
90X-RAY DIFFRACTION90O50 - 73
91X-RAY DIFFRACTION91O74 - 88
92X-RAY DIFFRACTION92P1 - 19
93X-RAY DIFFRACTION93P20 - 43
94X-RAY DIFFRACTION94P44 - 52
95X-RAY DIFFRACTION95P53 - 62
96X-RAY DIFFRACTION96P63 - 83
97X-RAY DIFFRACTION97Q2 - 17
98X-RAY DIFFRACTION98Q18 - 82
99X-RAY DIFFRACTION99Q83 - 100
100X-RAY DIFFRACTION100R19 - 23
101X-RAY DIFFRACTION101R24 - 28
102X-RAY DIFFRACTION102R29 - 36
103X-RAY DIFFRACTION103R37 - 43
104X-RAY DIFFRACTION104R44 - 52
105X-RAY DIFFRACTION105R53 - 76
106X-RAY DIFFRACTION106R77 - 88
107X-RAY DIFFRACTION107S2 - 12
108X-RAY DIFFRACTION108S13 - 25
109X-RAY DIFFRACTION109S26 - 35
110X-RAY DIFFRACTION110S36 - 40
111X-RAY DIFFRACTION111S41 - 70
112X-RAY DIFFRACTION112S71 - 81
113X-RAY DIFFRACTION113T8 - 66
114X-RAY DIFFRACTION114T67 - 75
115X-RAY DIFFRACTION115T76 - 91
116X-RAY DIFFRACTION116T92 - 106
117X-RAY DIFFRACTION117U2 - 8
118X-RAY DIFFRACTION118U9 - 15
119X-RAY DIFFRACTION119U16 - 25
120X-RAY DIFFRACTION120a1 - 3
121X-RAY DIFFRACTION121b33 - 38

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る