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- PDB-5w4u: Pol II elongation complex with an N6-methyladenine-containing template -

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基本情報

登録情報
データベース: PDB / ID: 5w4u
タイトルPol II elongation complex with an N6-methyladenine-containing template
要素
  • (DNA-directed RNA polymerase II subunit ...) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • 14mer non-template DNA
  • 29mer template DNA
  • 9mer RNA
キーワードDNA BINDING PROTEIN/RNA/DNA / Complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-RNA-DNA complex
機能・相同性
機能・相同性情報


RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / RNA Polymerase II Promoter Escape ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / translesion synthesis / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / ribosome biogenesis / peroxisome / nucleic acid binding / transcription by RNA polymerase II / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
類似検索 - 分子機能
Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 ...Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Gyrase A; domain 2 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / : / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / Homeodomain-like / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / Zinc finger, TFIIS-type / DNA-directed RNA polymerase, RBP11-like dimerisation domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb3/Rpb11 dimerisation domain / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Single Sheet / Nucleic acid-binding proteins / Beta Complex / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 ...DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.6 Å
データ登録者Wang, W. / Wang, D.
引用ジャーナル: J.Am.Chem.Soc. / 年: 2017
タイトル: Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing.
著者: Wang, W. / Xu, L. / Hu, L. / Chong, J. / He, C. / Wang, D.
履歴
登録2017年6月13日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年6月20日Provider: repository / タイプ: Initial release
改定 1.12019年7月3日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22023年10月4日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_type.id

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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: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
T: 29mer template DNA
N: 14mer non-template DNA
R: 9mer RNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)486,30122
ポリマ－485,75313
非ポリマー5489
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area65220 Å2
ΔGint-394 kcal/mol
Surface area141090 Å2
単位格子
Length a, b, c (Å)167.210, 221.990, 192.700
Angle α, β, γ (deg.)90.00, 100.58, 90.00
Int Tables number5
Space group name H-MC121

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要素

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DNA-directed RNA polymerase II subunit ... , 5種, 5分子 ABCIK

#1: タンパク質 DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


分子量: 191821.578 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P04050, DNA-directed RNA polymerase
#2: タンパク質 DNA-directed RNA polymerase II subunit RPB2 / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


分子量: 138937.297 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P08518, DNA-directed RNA polymerase
#3: タンパク質 DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


分子量: 35330.457 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P16370
#7: タンパク質 DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA- ...RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


分子量: 14308.161 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P27999
#9: タンパク質 DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


分子量: 13633.493 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P38902

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DNA-directed RNA polymerases I, II, and III subunit ... , 5種, 5分子 EFHJL

#4: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


分子量: 25117.094 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P20434
#5: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


分子量: 17931.834 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P20435
#6: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


分子量: 16525.363 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P20436
#8: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide


分子量: 8290.732 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P22139
#10: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


分子量: 7729.969 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P40422

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DNA鎖 , 2種, 2分子 TN

#11: DNA鎖 29mer template DNA


分子量: 8865.777 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Saccharomyces cerevisiae (パン酵母)
#12: DNA鎖 14mer non-template DNA


分子量: 4286.789 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Saccharomyces cerevisiae (パン酵母)

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RNA鎖 , 1種, 1分子 R

#13: RNA鎖 9mer RNA


分子量: 2974.854 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Saccharomyces cerevisiae (パン酵母)

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非ポリマー , 2種, 9分子

#14: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Zn / タイプ: SUBJECT OF INVESTIGATION
#15: 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: 1 / 由来タイプ: 合成 / 式: Mg / タイプ: SUBJECT OF INVESTIGATION

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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: 3.62 Å3/Da / 溶媒含有率: 66.01 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5
詳細: 390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 10-12.5% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: ALS / ビームライン: 8.2.1 / 波長: 1 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2015年8月22日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 3.6→95.8 Å / Num. obs: 79907 / % possible obs: 100 % / 冗長度: 5.4 % / Net I/σ(I): 5

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解析

ソフトウェア
名称バージョン分類
PHENIX1.8.4_1496精密化
MOSFLMデータ削減
SCALAデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 2NVZ

2nvz


解像度: 3.6→81.021 Å / SU ML: 0.44 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.56 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2591 3545 4.97 %
Rwork0.227 --
obs0.2286 71390 89.37 %
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: 3.6→81.021 Å
タンパク質核酸リガンド溶媒全体
原子数27742 1070 9 0 28821
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00229449
X-RAY DIFFRACTIONf_angle_d0.51439990
X-RAY DIFFRACTIONf_dihedral_angle_d12.21411253
X-RAY DIFFRACTIONf_chiral_restr0.0214495
X-RAY DIFFRACTIONf_plane_restr0.0024989
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6004-3.64980.3391470.3161648X-RAY DIFFRACTION21
3.6498-3.70190.3407540.31481236X-RAY DIFFRACTION41
3.7019-3.75720.3378870.29081679X-RAY DIFFRACTION54
3.7572-3.81590.3091810.2961940X-RAY DIFFRACTION65
3.8159-3.87840.31291080.30682280X-RAY DIFFRACTION75
3.8784-3.94530.38321530.30162552X-RAY DIFFRACTION85
3.9453-4.0170.3171580.28282821X-RAY DIFFRACTION94
4.017-4.09430.29231500.27433084X-RAY DIFFRACTION100
4.0943-4.17790.29031750.2672978X-RAY DIFFRACTION100
4.1779-4.26870.29731820.25333010X-RAY DIFFRACTION100
4.2687-4.3680.25761490.23483015X-RAY DIFFRACTION100
4.368-4.47720.25391280.22463076X-RAY DIFFRACTION100
4.4772-4.59830.2331460.21663025X-RAY DIFFRACTION100
4.5983-4.73360.23241540.20283033X-RAY DIFFRACTION100
4.7336-4.88630.24731750.20843024X-RAY DIFFRACTION100
4.8863-5.0610.23181630.21573019X-RAY DIFFRACTION100
5.061-5.26360.25991620.21833010X-RAY DIFFRACTION100
5.2636-5.50310.27921450.22333071X-RAY DIFFRACTION100
5.5031-5.79310.2841500.22843067X-RAY DIFFRACTION100
5.7931-6.1560.25351530.22393015X-RAY DIFFRACTION100
6.156-6.63110.2281690.22993052X-RAY DIFFRACTION100
6.6311-7.2980.2441490.2173062X-RAY DIFFRACTION100
7.298-8.35310.18771570.17573045X-RAY DIFFRACTION100
8.3531-10.52040.19921780.15023042X-RAY DIFFRACTION100
10.5204-81.04120.22491720.19273061X-RAY DIFFRACTION99
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)
11.34090.4664-0.15131.82760.32041.870.0950.14660.48060.1670.0472-0.8462-0.39361.2726-0.07790.5096-0.1507-0.03871.5468-0.01521.842482.8626-15.1367418.3323
22.31640.6317-0.01361.5208-0.22421.60990.28070.25960.05930.0708-0.0407-0.14140.39530.1536-0.13760.31050.0453-0.06990.1339-0.00840.247439.1414-41.0048411.7024
30.212-0.0968-0.17751.76430.38010.80170.2346-0.3349-0.1820.87220.0134-0.19330.5424-0.2852-0.0450.6347-0.1665-0.02340.35180.18430.347425.7122-34.1069444.6311
40.38080.01010.23371.2033-0.37070.50780.0935-0.1277-0.14080.58360.15660.05590.47150.0211-0.06181.10110.1624-0.36540.21280.04120.6576450.253-57.2259448.7079
51.84140.5991.49855.93584.16634.36220.0692-0.4882-0.09810.96590.0628-0.23830.40040.0058-0.11951.80620.0834-0.27040.574-0.03810.833458.9598-13.3278487.4616
60.4320.0903-0.4291.11311.26892.1878-0.0558-0.28180.1040.97830.0891-0.3313-0.2593-0.013-0.17941.2240.2273-0.40690.4644-0.070.6435453.0298-39.7776458.272
70.98050.2529-0.27840.6119-1.18482.75620.05180.2130.38730.72870.348-1.03130.04960.8201-0.0570.4760.1298-0.26280.6504-0.02530.942468.4351-36.7139424.3464
82.17150.71530.13372.3032-0.79261.54770.2673-0.28550.46060.2384-0.1717-0.2024-0.69610.0515-0.16290.7667-0.17690.37460.15890.06730.3985427.04314.2795431.2409
91.15531.28360.22312.4715-0.12740.1923-0.00820.25660.4874-0.44290.0650.0679-0.49540.1449-0.07690.6907-0.17280.21740.37970.19050.4502430.906815.3988411.8725
101.47480.62421.8060.8591.83844.26480.235-0.19530.07790.45260.2288-0.36980.21970.4321-0.36171.0374-0.1751-0.11540.3404-0.06140.6811452.71266.2615451.8872
114.33570.08230.87953.5485-0.44346.8327-0.21570.5060.43560.4371-0.1167-0.6911-0.92621.04980.3360.9964-0.19080.00850.5571-0.07070.752461.859716.7305456.7429
120.57870.18190.77890.93660.17561.00850.32760.10860.24240.05050.2699-0.2686-0.15580.2428-0.29780.5995-0.17960.15230.45440.08910.7832448.059610.6563433.6014
130.8260.3333-0.4821.09640.07091.82850.0841-0.19890.01570.1916-0.0165-0.2024-0.19680.24120.12850.309-0.03970.26420.14760.11650.2464432.3235-0.8315434.2175
146.66050.80132.47743.21222.05613.84280.0348-0.73490.40910.54060.1748-0.1729-0.1147-0.0937-0.15530.8132-0.02450.16650.2652-0.02010.3935433.169417.2989455.6366
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160.71630.08880.53471.6268-0.0290.96490.0197-0.07020.19830.72920.06450.0837-0.0036-0.4240.01830.3385-0.00910.36610.31890.14110.1042417.9754-8.9687436.6544
170.5535-0.04420.43771.23180.02141.18440.13480.2661-0.0067-0.45250.0658-0.1822-0.30620.3260.02550.3423-0.24650.28950.49940.15770.0884426.3051-14.4533406.8364
181.66310.9889-1.12032.5253-1.00572.6511-0.09950.23640.0329-0.29840.0712-0.19090.03520.13240.01110.2325-0.03650.01230.37830.10480.2298427.058-17.2997405.0901
190.2609-0.03810.61891.1913-0.06181.28260.12070.26590.19320.0762-0.0598-0.45750.170.3242-0.08330.1692-0.11150.05020.29380.14940.4188442.9426-28.7934415.4331
202.12290.4806-0.75151.7088-0.49061.3827-0.2248-0.2323-0.1958-0.23430.00690.5620.0878-0.5194-0.18520.2832-0.3014-0.19170.93840.20010.3472395.3801-38.4604404.8713
211.27690.3786-0.41312.90290.43121.4286-0.0210.61080.0235-0.23-0.07610.3326-0.1187-0.47350.08490.24630.0431-0.02580.76120.13610.298403.9252-18.5088392.66
221.89050.8492-0.64573.7434-0.76811.9690.0214-0.2895-0.18930.5981-0.15720.52510.0573-0.2799-0.04630.4193-0.41690.03980.71320.19130.4725396.0607-41.1208429.6132
232.9172-2.02271.72194.8924-1.42234.0206-0.0772-0.2753-0.74210.6997-0.01490.1370.0247-0.44820.07490.7396-0.5023-0.15081.27860.24311.0438389.7-51.9929426.9864
241.9119-1.21350.68333.8831-1.75960.92550.29490.5716-0.0982-0.9004-0.23730.51730.2815-0.1186-0.03240.4325-0.2913-0.20960.7042-0.05540.502399.4254-44.7862398.3283
251.52070.2360.14210.08610.39762.8728-0.4331-0.8260.33020.7310.2459-0.1725-0.19490.3794-0.12181.84740.4033-1.0141.1874-0.2721.2353474.9314-49.4736475.4678
260.3487-0.48350.1061.0205-0.35380.15280.1483-0.58450.4881.00440.8116-1.39570.39480.6329-0.82441.47410.2672-0.84811.4951-0.39661.9016484.5502-44.9416468.3482
270.3504-0.4657-0.99130.67621.38662.88810.0888-0.6508-0.04180.56790.531-1.33040.12970.7548-0.65411.534-0.0544-0.83562.0888-0.56072.7217493.2162-39.4479469.4624
281.2862-1.3963-0.6941.62130.35481.8091-0.054-0.07090.98351.01740.5882-1.450.09940.9628-0.07041.14460.3005-0.71770.9681-0.16831.5494478.8803-44.8491458.5649
290.9558-0.99440.26631.1478-0.54970.695-0.08310.03690.49610.3226-0.0892-0.7981-0.0460.38160.39691.00860.3446-0.65710.4729-0.05911.0612471.6364-48.8204446.5715
305.7571-2.03991.22992.5866-1.64313.6760.08050.0707-0.23510.67970.1506-1.11360.54690.7551-0.07470.90130.2253-0.26120.4442-0.02470.6986461.7006-59.472415.5602
313.8007-0.85721.49162.0868-0.53180.61770.31420.4106-0.8545-0.6075-0.1553-0.45930.68610.3918-0.12951.07210.244-0.06270.7274-0.06750.8085450.5956-61.9153398.2078
321.7792-1.60231.40618.2167-8.09697.9999-0.0592-0.0907-1.29990.50050.30671.36710.5386-0.1397-0.23510.98270.3204-0.21920.4198-0.0620.8712449.564-61.3573406.0789
333.0518-1.95690.6074.50482.22482.2407-0.1537-0.2469-0.2177-0.30860.72-0.24740.5060.2351-0.49930.9420.0651-0.02640.4743-0.0070.4872462.7757-61.7252411.9736
346.6906-5.0118-7.76715.18966.99589.98321.1064-1.6456-0.24780.5399-0.6541-2.0892-0.02981.023-0.4050.5067-0.19930.02950.81740.26911.4405473.6782-53.6918425.1526
353.5746-1.9773-1.76037.7884-0.9599.46510.3664-0.0235-0.00820.01690.1746-0.2897-0.25790.2987-0.45191.45780.5026-0.21020.7548-0.21611.0407468.8419-61.9447418.3065
369.00944.9645-1.06796.5648-4.44784.95950.58650.8605-0.1799-0.1086-0.3461.2299-0.4699-0.5611-0.29211.05480.3931-0.30530.5348-0.13670.8999456.8794-65.8527417.1049
373.0881-0.635-1.71683.2846-1.91632.59240.2497-0.7116-0.09180.7801-0.44310.64060.4755-0.05410.12251.0253-0.53420.18021.04730.19930.9395405.1453-67.484444.0755
382.24810.8909-1.24275.6892-1.32951.74730.1841-0.7098-0.3850.7947-0.24320.16650.15460.1260.03341.2318-0.5068-0.03540.67480.41081.1527402.795-70.7426443.9106
395.90226.2857-5.44978.1967-6.3635.2394-0.21050.077-0.4749-0.7525-0.13610.18040.06590.03630.28851.9278-0.3628-0.29530.61410.18091.3664409.683-74.3948420.3114
404.38394.074-5.45958.6515-6.20867.4574-0.23560.89940.7338-1.33120.80720.3368-0.6291-0.3242-0.56051.9447-0.7246-0.01620.9908-0.02322.0285399.4971-77.2521421.742
411.66761.148-1.12614.273-1.35922.1030.0325-0.1994-0.2956-0.0293-0.11570.00220.09250.15610.00661.4118-0.2426-0.30340.59090.4491.0808412.6908-72.573437.4437
425.1957-1.81961.44568.631.17494.4562-0.497-0.8097-1.00970.92550.08650.36980.96350.03510.29071.3694-0.24-0.12320.70980.5071.291417.2359-75.9599446.3547
432.7335-2.66030.06469.4543-2.57063.34810.0208-0.0992-1.008-0.59170.582-0.11731.4495-0.1241-0.47631.5926-0.4428-0.2420.86250.2910.8946415.1328-76.2921440.1852
447.2936.6066-2.2817.548-3.25555.48620.4222-0.23950.75391.2092-0.02981.25230.5012-0.7715-0.56211.3208-0.29840.16970.48790.28051.4179401.3549-74.6484435.5768
450.48520.3505-0.50945.15550.02650.655-0.0084-0.1307-0.01410.26920.1847-0.23070.18110.1895-0.17221.46-0.1345-0.20580.5808-0.33470.7037459.947810.2393482.5165
465.4592-0.9285-3.14933.8373.03444.82980.6113-0.26320.2511-0.4008-0.31510.0851-0.27590.3047-0.25920.8180.01780.09640.5489-0.03970.3266423.57751.3983471.6534
473.2614-4.8394-2.80038.25375.02858.87530.1437-0.2670.24740.18630.4216-0.63720.63430.7148-0.43710.4396-0.12580.16740.6848-0.06270.398431.3361-5.2202473.2523
481.005-0.1629-1.51230.2841-0.0287.31250.0919-0.24060.01290.0521-0.1683-0.0602-0.1280.7805-0.04560.36870.02310.33080.32330.08290.2681407.1921-12.7476407.1217
491.1628-1.4852.86081.9752-3.82027.3912-0.21980.37180.1268-0.03160.02660.2130.0117-0.36770.13210.1862-0.02790.04550.61110.04080.4613404.827-24.096409.6632
504.19841.0328-1.6232.1892-0.73.27030.22610.46980.1971-0.0103-0.27410.2308-0.1646-0.55980.10390.20030.08630.2670.4229-0.06480.4686398.2573-18.7311407.4062
515.30610.76421.34832.0603-1.92683.72550.1046-0.03040.57850.37620.04650.9248-0.5556-0.7467-0.22430.25870.21290.2120.7482-0.11020.677395.3195-7.3269412.8517
529.49643.67142.49289.51976.62484.6106-0.16080.41360.5174-0.1883-0.4732-0.4944-0.80930.89120.61360.54650.1920.07961.1970.29261.3762389.4303-5.5259419.0823
530.7447-0.0301-0.85692.78611.61233.0658-0.1077-0.04170.09630.0079-0.00910.2559-0.0401-0.2893-0.08070.1254-0.0140.11770.7541-0.01260.734393.4445-17.5879417.1459
541.9962-0.38180.79560.9986-0.36340.39260.1342-0.2005-0.13610.0857-0.05440.09370.04470.04330.06560.3324-0.05430.15810.48250.110.2027401.8239-19.8389417.1613
551.96532.1881-0.84852.7046-0.67810.63390.16960.69770.67480.16010.20840.4619-0.2125-0.1661-0.37150.3247-0.26620.30520.4760.03030.4048407.5315-9.2851413.6073
569.02120.50641.98112.3073-0.48252.0628-0.02120.33370.6353-0.61170.32920.2255-0.7117-0.3646-0.27550.3520.03460.05660.43780.18760.685411.82181.4591405.8487
573.6442-1.4608-0.08284.680.64085.3638-0.37290.5334-0.1536-0.3366-0.2653-0.1692-0.3931-0.86020.62910.4273-0.0383-0.02540.5244-0.01450.3479421.2451-34.4891398.7929
584.95010.73311.05345.02381.12553.12460.58490.3362-0.67740.0193-0.4114-1.11530.54020.2094-0.06940.3421-0.21030.0790.7195-0.04550.7328418.2311-56.079397.8974
596.14282.06250.98952.9862-3.29176.00520.3260.0928-0.28950.6620.3841-0.44310.4465-0.1842-0.59340.5546-0.0402-0.11650.4943-0.05840.2344414.7352-53.1731400.8798
600.2650.3846-0.17824.86770.85560.4075-0.02490.0442-0.49590.3096-0.2770.66470.2612-0.34490.24810.5256-0.3101-0.09360.39970.04750.5837405.6065-52.9085407.2467
611.16160.312-1.14814.18511.96362.38980.05320.2147-0.61910.1531-0.19870.8980.6205-0.82210.2290.7377-0.2694-0.39770.57610.04130.953406.7307-62.491409.8102
625.97654.81854.38865.15335.31525.7120.08480.3692-0.61550.02540.2334-0.33460.6030.2611-0.36690.578-0.0887-0.2560.2533-0.0580.3445420.8252-44.5787406.9489
631.8163-0.58770.88432.43950.88572.51820.36870.1182-0.82180.010.14970.0050.7493-0.1391-0.19610.6307-0.0689-0.35560.3495-0.16920.4726414.5086-58.4279405.6235
644.3777-0.6699-2.71484.02023.90274.78830.27070.6602-0.99520.0429-0.09290.24970.8082-0.0731-0.16961.2397-0.2292-0.30980.8665-0.18381.444407.8509-72.5013402.6983
652.431-0.33730.50050.5855-0.15041.6050.56070.6764-1.0175-0.0474-0.46731.00460.4771-0.6565-0.00990.402-0.2345-0.05650.8653-0.02980.8598391.744-49.8053400.8486
662.96740.91931.93778.5833-6.14397.53960.7060.850.1591-0.3291-0.1380.0476-1.0999-0.3721-0.52661.2139-0.0628-0.29571.31440.56371.0768425.91973.4231387.4775
675.7345-2.874-4.70134.4391-1.19579.10040.1470.4311.1011-1.0239-0.4391.4614-1.6476-2.42360.27881.71120.0994-0.19081.52590.30561.3427420.4519.3367394.5013
687.46115.71486.81074.37815.21556.21840.13620.94550.6128-0.7555-0.0046-0.3037-0.63640.1573-0.13741.7329-0.23640.03461.43920.72451.2688426.41547.4172383.9132
699.44450.1958-4.61087.8447-2.32662.89180.71820.53530.6478-0.96680.022-0.8508-1.3371-0.0605-0.76912.3295-0.37220.19911.8108-0.06962.237436.06668.8844385.1766
703.38553.259-1.80727.53040.9662.6360.35250.37471.1052-0.23790.00450.0533-1.2283-0.454-0.36282.0598-0.02760.2461.38780.50051.7957425.62215.5998390.8003
715.2712.0412-0.66494.3869-4.14435.81380.2893-0.86320.41530.6643-0.6269-0.0706-1.8310.56870.28541.0175-0.21620.02110.89570.2320.3612428.20598.1854394.8289
721.46762.8585-0.8776.4155-2.00070.6242-0.4120.45010.0334-1.6830.0261-0.19980.21440.12150.31770.88160.0636-0.0461.16990.13020.2913418.8425-14.7781388.8723
732.146-0.4158-1.15993.6022-0.10980.6659-0.1988-1.38040.48671.63420.0253-1.0815-0.27110.64590.1683.6425-0.0668-0.71343.3621-0.3233.0259490.8869-12.8229466.4897
742.6944-0.1062-2.16568.3335-1.77863.9442-0.05910.53910.1294-0.0797-0.15350.42450.12720.19460.13383.23760.0348-0.30093.1735-0.21712.9426470.477-13.7923452.44
754.69051.3982-0.1733.5581.21050.5146-0.5985-0.5021.03750.78570.039-1.6628-1.32991.15980.52971.1-0.1174-0.3850.8792-0.1041.0071449.2591-14.287420.2533
760.1498-0.8010.56514.5957-1.708770.05850.42480.7628-0.3615-0.3762-0.1182-0.59850.36890.33332.33250.57710.00732.877-0.11582.7864479.9071-15.945457.0712
771.1345-1.40.76652.31880.87776.1395-0.2507-0.3301-0.1943-0.653-0.1036-0.789-0.23841.6110.31120.5090.03640.10010.6171-0.02440.6689444.1613-13.0768418.4428
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 304 )
2X-RAY DIFFRACTION2chain 'A' and (resid 305 through 578 )
3X-RAY DIFFRACTION3chain 'A' and (resid 579 through 844 )
4X-RAY DIFFRACTION4chain 'A' and (resid 845 through 1166 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1167 through 1268 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1269 through 1376 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1377 through 1449 )
8X-RAY DIFFRACTION8chain 'B' and (resid 20 through 94 )
9X-RAY DIFFRACTION9chain 'B' and (resid 95 through 202 )
10X-RAY DIFFRACTION10chain 'B' and (resid 203 through 307 )
11X-RAY DIFFRACTION11chain 'B' and (resid 308 through 371 )
12X-RAY DIFFRACTION12chain 'B' and (resid 372 through 479 )
13X-RAY DIFFRACTION13chain 'B' and (resid 480 through 559 )
14X-RAY DIFFRACTION14chain 'B' and (resid 560 through 633 )
15X-RAY DIFFRACTION15chain 'B' and (resid 634 through 700 )
16X-RAY DIFFRACTION16chain 'B' and (resid 701 through 791 )
17X-RAY DIFFRACTION17chain 'B' and (resid 792 through 892 )
18X-RAY DIFFRACTION18chain 'B' and (resid 893 through 1022 )
19X-RAY DIFFRACTION19chain 'B' and (resid 1023 through 1220 )
20X-RAY DIFFRACTION20chain 'C' and (resid 3 through 51 )
21X-RAY DIFFRACTION21chain 'C' and (resid 52 through 176 )
22X-RAY DIFFRACTION22chain 'C' and (resid 177 through 207 )
23X-RAY DIFFRACTION23chain 'C' and (resid 208 through 227 )
24X-RAY DIFFRACTION24chain 'C' and (resid 228 through 268 )
25X-RAY DIFFRACTION25chain 'E' and (resid 3 through 71 )
26X-RAY DIFFRACTION26chain 'E' and (resid 72 through 89 )
27X-RAY DIFFRACTION27chain 'E' and (resid 90 through 103 )
28X-RAY DIFFRACTION28chain 'E' and (resid 104 through 167 )
29X-RAY DIFFRACTION29chain 'E' and (resid 168 through 215 )
30X-RAY DIFFRACTION30chain 'F' and (resid 72 through 102 )
31X-RAY DIFFRACTION31chain 'F' and (resid 103 through 116 )
32X-RAY DIFFRACTION32chain 'F' and (resid 117 through 126 )
33X-RAY DIFFRACTION33chain 'F' and (resid 127 through 137 )
34X-RAY DIFFRACTION34chain 'F' and (resid 138 through 142 )
35X-RAY DIFFRACTION35chain 'F' and (resid 143 through 147 )
36X-RAY DIFFRACTION36chain 'F' and (resid 148 through 155 )
37X-RAY DIFFRACTION37chain 'H' and (resid 3 through 30 )
38X-RAY DIFFRACTION38chain 'H' and (resid 31 through 60 )
39X-RAY DIFFRACTION39chain 'H' and (resid 61 through 82 )
40X-RAY DIFFRACTION40chain 'H' and (resid 83 through 92 )
41X-RAY DIFFRACTION41chain 'H' and (resid 93 through 106 )
42X-RAY DIFFRACTION42chain 'H' and (resid 107 through 118 )
43X-RAY DIFFRACTION43chain 'H' and (resid 119 through 140 )
44X-RAY DIFFRACTION44chain 'H' and (resid 141 through 146 )
45X-RAY DIFFRACTION45chain 'I' and (resid 2 through 52 )
46X-RAY DIFFRACTION46chain 'I' and (resid 53 through 86 )
47X-RAY DIFFRACTION47chain 'I' and (resid 87 through 116 )
48X-RAY DIFFRACTION48chain 'J' and (resid 1 through 5 )
49X-RAY DIFFRACTION49chain 'J' and (resid 6 through 10 )
50X-RAY DIFFRACTION50chain 'J' and (resid 11 through 17 )
51X-RAY DIFFRACTION51chain 'J' and (resid 18 through 26 )
52X-RAY DIFFRACTION52chain 'J' and (resid 27 through 31 )
53X-RAY DIFFRACTION53chain 'J' and (resid 32 through 43 )
54X-RAY DIFFRACTION54chain 'J' and (resid 44 through 51 )
55X-RAY DIFFRACTION55chain 'J' and (resid 52 through 56 )
56X-RAY DIFFRACTION56chain 'J' and (resid 57 through 65 )
57X-RAY DIFFRACTION57chain 'K' and (resid 1 through 9 )
58X-RAY DIFFRACTION58chain 'K' and (resid 10 through 29 )
59X-RAY DIFFRACTION59chain 'K' and (resid 30 through 39 )
60X-RAY DIFFRACTION60chain 'K' and (resid 40 through 50 )
61X-RAY DIFFRACTION61chain 'K' and (resid 51 through 62 )
62X-RAY DIFFRACTION62chain 'K' and (resid 63 through 69 )
63X-RAY DIFFRACTION63chain 'K' and (resid 70 through 77 )
64X-RAY DIFFRACTION64chain 'K' and (resid 78 through 82 )
65X-RAY DIFFRACTION65chain 'K' and (resid 83 through 114 )
66X-RAY DIFFRACTION66chain 'L' and (resid 27 through 31 )
67X-RAY DIFFRACTION67chain 'L' and (resid 32 through 36 )
68X-RAY DIFFRACTION68chain 'L' and (resid 37 through 41 )
69X-RAY DIFFRACTION69chain 'L' and (resid 42 through 46 )
70X-RAY DIFFRACTION70chain 'L' and (resid 47 through 51 )
71X-RAY DIFFRACTION71chain 'L' and (resid 52 through 58 )
72X-RAY DIFFRACTION72chain 'L' and (resid 59 through 70 )
73X-RAY DIFFRACTION73chain 'T' and (resid 1 through 6 )
74X-RAY DIFFRACTION74chain 'T' and (resid 8 through 14 )
75X-RAY DIFFRACTION75chain 'T' and (resid 15 through 29 )
76X-RAY DIFFRACTION76chain 'N' and (resid 1 through 14 )
77X-RAY DIFFRACTION77chain 'R' and (resid 1 through 9 )

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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://pdbjlvh1.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