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- PDB-3zni: Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex -

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基本情報

登録情報
データベース: PDB / ID: 3zni
タイトルStructure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex
要素
  • E3 UBIQUITIN-PROTEIN LIGASE CBL-B
  • POLYUBIQUITIN-C
  • TYROSINE-PROTEIN KINASE ZAP-70
  • UBIQUITIN-CONJUGATING ENZYME E2 D2
キーワードLIGASE / LIGASES / DEGRADATION
機能・相同性
機能・相同性情報


T cell aggregation / regulation of platelet-derived growth factor receptor-alpha signaling pathway / T cell anergy / positive regulation of T cell anergy / positive regulation of alpha-beta T cell proliferation / CD4-positive, alpha-beta T cell proliferation / negative thymic T cell selection / (E3-independent) E2 ubiquitin-conjugating enzyme / negative regulation of CD4-positive, alpha-beta T cell proliferation / beta selection ...T cell aggregation / regulation of platelet-derived growth factor receptor-alpha signaling pathway / T cell anergy / positive regulation of T cell anergy / positive regulation of alpha-beta T cell proliferation / CD4-positive, alpha-beta T cell proliferation / negative thymic T cell selection / (E3-independent) E2 ubiquitin-conjugating enzyme / negative regulation of CD4-positive, alpha-beta T cell proliferation / beta selection / positive thymic T cell selection / positive regulation of alpha-beta T cell differentiation / positive regulation of T cell differentiation / T cell receptor complex / negative regulation of T cell receptor signaling pathway / E2 ubiquitin-conjugating enzyme / NLS-bearing protein import into nucleus / Translocation of ZAP-70 to Immunological synapse / extrinsic component of cytoplasmic side of plasma membrane / B cell activation / ubiquitin conjugating enzyme activity / RHOH GTPase cycle / Generation of second messenger molecules / immunological synapse / T cell differentiation / T cell migration / protein autoubiquitination / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / cell surface receptor protein tyrosine kinase signaling pathway / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / phosphotyrosine residue binding / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of calcium-mediated signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / T cell activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / positive regulation of protein ubiquitination / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling
類似検索 - 分子機能
E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / Adaptor protein Cbl, N-terminal domain / Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain ...E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / Adaptor protein Cbl, N-terminal domain / Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. / Prokaryotic RING finger family 4 / Adaptor protein Cbl, N-terminal domain superfamily / Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain / Transcription Elongation Factor S-II; Chain A / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / SH2 domain / SHC Adaptor Protein / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Herpes Virus-1 / Ubiquitin-conjugating enzyme/RWD-like / : / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / SH2 domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / : / Ubiquitin domain signature. / Ubiquitin conserved site / SH2 domain superfamily / Ubiquitin domain / Ubiquitin-like (UB roll) / EF-hand domain pair / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Polyubiquitin-C / Tyrosine-protein kinase ZAP-70 / Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase CBL-B
類似検索 - 構成要素
生物種HOMO SAPIENS (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.21 Å
データ登録者Dou, H. / Buetow, L. / Sibbet, G.J. / Cameron, K. / Huang, D.T.
引用ジャーナル: Nat.Struct.Mol.Biol. / 年: 2013
タイトル: Essentiality of a Non-Ring Element in Priming Donor Ubiquitin for Catalysis by a Monomeric E3.
著者: Dou, H. / Buetow, L. / Sibbet, G.J. / Cameron, K. / Huang, D.T.
履歴
登録2013年2月14日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02013年7月10日Provider: repository / タイプ: Initial release
改定 1.12013年7月17日Group: Database references
改定 1.22013年7月24日Group: Database references / Other / Source and taxonomy
改定 1.32013年8月21日Group: Database references
改定 1.42015年9月23日Group: Data collection
改定 1.52017年9月13日Group: Data collection / カテゴリ: diffrn_detector / Item: _diffrn_detector.type
改定 1.62019年7月31日Group: Advisory / Data collection / Derived calculations
カテゴリ: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn_type.id
改定 1.72023年12月20日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: E3 UBIQUITIN-PROTEIN LIGASE CBL-B
B: TYROSINE-PROTEIN KINASE ZAP-70
C: UBIQUITIN-CONJUGATING ENZYME E2 D2
D: POLYUBIQUITIN-C
E: E3 UBIQUITIN-PROTEIN LIGASE CBL-B
F: TYROSINE-PROTEIN KINASE ZAP-70
G: UBIQUITIN-CONJUGATING ENZYME E2 D2
H: POLYUBIQUITIN-C
I: E3 UBIQUITIN-PROTEIN LIGASE CBL-B
J: TYROSINE-PROTEIN KINASE ZAP-70
K: UBIQUITIN-CONJUGATING ENZYME E2 D2
L: POLYUBIQUITIN-C
M: E3 UBIQUITIN-PROTEIN LIGASE CBL-B
N: TYROSINE-PROTEIN KINASE ZAP-70
O: UBIQUITIN-CONJUGATING ENZYME E2 D2
P: POLYUBIQUITIN-C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)291,87132
ポリマ－290,94016
非ポリマー93216
水13,691760
1
A: E3 UBIQUITIN-PROTEIN LIGASE CBL-B
B: TYROSINE-PROTEIN KINASE ZAP-70
C: UBIQUITIN-CONJUGATING ENZYME E2 D2
D: POLYUBIQUITIN-C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)72,9688
ポリマ－72,7354
非ポリマー2334
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-24.8 kcal/mol
Surface area34780 Å2
手法PQS
2
E: E3 UBIQUITIN-PROTEIN LIGASE CBL-B
F: TYROSINE-PROTEIN KINASE ZAP-70
G: UBIQUITIN-CONJUGATING ENZYME E2 D2
H: POLYUBIQUITIN-C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)72,9688
ポリマ－72,7354
非ポリマー2334
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-28.4 kcal/mol
Surface area34500 Å2
手法PQS
3
I: E3 UBIQUITIN-PROTEIN LIGASE CBL-B
J: TYROSINE-PROTEIN KINASE ZAP-70
K: UBIQUITIN-CONJUGATING ENZYME E2 D2
L: POLYUBIQUITIN-C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)72,9688
ポリマ－72,7354
非ポリマー2334
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-29.7 kcal/mol
Surface area34160 Å2
手法PQS
4
M: E3 UBIQUITIN-PROTEIN LIGASE CBL-B
N: TYROSINE-PROTEIN KINASE ZAP-70
O: UBIQUITIN-CONJUGATING ENZYME E2 D2
P: POLYUBIQUITIN-C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)72,9688
ポリマ－72,7354
非ポリマー2334
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-23.2 kcal/mol
Surface area34930 Å2
手法PQS
単位格子
Length a, b, c (Å)94.970, 131.800, 122.000
Angle α, β, γ (deg.)90.00, 91.92, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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タンパク質 , 3種, 12分子 AEIMCGKODHLP

#1: タンパク質
E3 UBIQUITIN-PROTEIN LIGASE CBL-B / CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE B / RING FINGER PROTEIN 56 / SH3-BINDING PROTEIN CBL-B / ...CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE B / RING FINGER PROTEIN 56 / SH3-BINDING PROTEIN CBL-B / SIGNAL TRANSDUCTION PROTEIN CBL-B


分子量: 45748.281 Da / 分子数: 4 / 断片: RESIDUES 36-427 / 変異: YES / 由来タイプ: 組換発現
詳細: Y363 IS PHOSPHORYLATED. GS AT THE N-TERMINUS OF PROTEIN RESULTED FROM CLONING.
由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q13191, ubiquitin-protein ligase
#3: タンパク質
UBIQUITIN-CONJUGATING ENZYME E2 D2 / UBIQUITIN CARRIER PROTEIN D2 / UBIQUITIN-CONJUGATING ENZYME E2(17)KB 2 / UBIQUITIN-CONJUGATING ...UBIQUITIN CARRIER PROTEIN D2 / UBIQUITIN-CONJUGATING ENZYME E2(17)KB 2 / UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2 / UBIQUITIN-PROTEIN LIGASE D2 / UBCH5B / P53-REGULATED UBIQUITIN-CONJUGATING ENZYME 1


分子量: 16720.186 Da / 分子数: 4 / 断片: RESIDUES 2-147 / 変異: YES / 由来タイプ: 組換発現
詳細: K85 SIDECHAIN IN CHIANS C, G, K AND O FORMS AN ISOPEPTIDE LINKAGE WITH THE CARBONYL CARBON OF G76 IN CHAINS D, H, L AND P, RESPECTIVELY.
由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P62837, ubiquitin-protein ligase
#4: タンパク質
POLYUBIQUITIN-C / UBIQUITIN


分子量: 8922.141 Da / 分子数: 4 / 断片: RESIDUES 77-152 / 由来タイプ: 組換発現
詳細: CARBONYL CARBON OF G76 IN CHIANS D, H, L AND P FORMS AN ISOPEPTIDE LINKAGE WITH THE SIDECHAIN OF K85 IN CHAINS C, G, K AND O, RESPECTIVELY. GSGGS LINKER AT THE N- TERMINUS OF PROTEIN RESULTED FROM CLONING
由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: P0CG48

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タンパク質・ペプチド , 1種, 4分子 BFJN

#2: タンパク質・ペプチド
TYROSINE-PROTEIN KINASE ZAP-70 / 70 KDA ZETA-CHAIN ASSOCIATED PROTEIN / SYK-RELATED TYROSINE KINASE


分子量: 1344.275 Da / 分子数: 4 / 断片: RESIDUES 286-297 / 由来タイプ: 合成
詳細: Y292 IS PHOSPHORYLATED. IN THE STRUCTURE Y292 IS NUMBERED AS 7.
由来: (合成) HOMO SAPIENS (ヒト)
参照: UniProt: P43403, non-specific protein-tyrosine kinase

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非ポリマー , 4種, 776分子

#5: 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
#6: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Ca
#7: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C2H6O2
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 760 / 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: 2.63 Å3/Da / 溶媒含有率: 54 % / 解説: NONE
結晶化詳細: 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE

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データ収集

回折
ID平均測定温度 (K)Crystal-ID
11001
21001
放射光源
由来サイトビームラインID波長
シンクロトロンDiamond I0410.9686
シンクロトロンDiamond I2420.9686
検出器
タイプID検出器日付
DECTRIS PILATUS 6M1PIXEL2012年10月15日
DECTRIS PILATUS3 6M2PIXEL
放射
IDプロトコル単色(M)・ラウエ(L)散乱光タイプWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
放射波長波長: 0.9686 Å / 相対比: 1
反射解像度: 2.21→30.5 Å / Num. obs: 149230 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / 冗長度: 3.4 % / Biso Wilson estimate: 41.76 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.2
反射 シェル解像度: 2.21→2.27 Å / 冗長度: 3.5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)精密化
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRIES 3PFV, 2LDR, 4A49 AND 4AUQ

3pfv

2ldr

4a49

4auq


解像度: 2.21→30.54 Å / SU ML: 0.26 / σ(F): 1.34 / 位相誤差: 23.79 / 立体化学のターゲット値: ML
詳細: FINAL MODEL CONTAINS FOLLOWING RESIDUES. CHAINS A, E, M RESIDUES 38 TO 427 AND CHAIN I RESIDUES 41 TO 426. CHAINS B AND N RESIDUES 4 TO 12 AND CHAINS F AND J RESIDUES 5 TO 12. CHAINS C, G, K ...詳細: FINAL MODEL CONTAINS FOLLOWING RESIDUES. CHAINS A, E, M RESIDUES 38 TO 427 AND CHAIN I RESIDUES 41 TO 426. CHAINS B AND N RESIDUES 4 TO 12 AND CHAINS F AND J RESIDUES 5 TO 12. CHAINS C, G, K AND O RESIDUES 2 TO 147. CHAINS D, H, L AND P RESIDUES 1 TO 76. ATOMS FROM RESIDUES WITH DISORDER SIDECHAIN ELECTRON DENSITY WERE OMITTED.
Rfactor反射数%反射
Rfree0.2114 7484 5 %
Rwork0.1748 --
obs0.1767 149230 99.58 %
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 mean: 48 Å2
精密化ステップサイクル: LAST / 解像度: 2.21→30.54 Å
タンパク質核酸リガンド溶媒全体
原子数19701 0 28 760 20489
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00420275
X-RAY DIFFRACTIONf_angle_d0.81127548
X-RAY DIFFRACTIONf_dihedral_angle_d13.3517530
X-RAY DIFFRACTIONf_chiral_restr0.0573010
X-RAY DIFFRACTIONf_plane_restr0.0043558
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.23510.33622530.27964698X-RAY DIFFRACTION100
2.2351-2.26140.27122410.26074761X-RAY DIFFRACTION100
2.2614-2.2890.30732540.25364693X-RAY DIFFRACTION100
2.289-2.31790.28012090.2544777X-RAY DIFFRACTION100
2.3179-2.34840.3162750.23724679X-RAY DIFFRACTION100
2.3484-2.38060.29512470.23624760X-RAY DIFFRACTION100
2.3806-2.41460.27622430.22364725X-RAY DIFFRACTION100
2.4146-2.45060.26162390.21784716X-RAY DIFFRACTION100
2.4506-2.48890.26092620.2174745X-RAY DIFFRACTION100
2.4889-2.52970.27522520.21464686X-RAY DIFFRACTION100
2.5297-2.57330.24262340.21074772X-RAY DIFFRACTION100
2.5733-2.620.27172600.21184715X-RAY DIFFRACTION100
2.62-2.67040.26572560.21614683X-RAY DIFFRACTION100
2.6704-2.72490.25062720.2114714X-RAY DIFFRACTION100
2.7249-2.78410.24252290.20634755X-RAY DIFFRACTION100
2.7841-2.84880.24882540.20664741X-RAY DIFFRACTION100
2.8488-2.920.24752340.20014733X-RAY DIFFRACTION100
2.92-2.99890.23772800.20184687X-RAY DIFFRACTION100
2.9989-3.0870.25292640.20334702X-RAY DIFFRACTION100
3.087-3.18660.23262410.19564740X-RAY DIFFRACTION100
3.1866-3.30030.24162540.19054746X-RAY DIFFRACTION100
3.3003-3.43230.21772470.17614681X-RAY DIFFRACTION100
3.4323-3.58830.20842440.17744761X-RAY DIFFRACTION99
3.5883-3.77720.21442550.16724727X-RAY DIFFRACTION100
3.7772-4.01330.1842410.14784735X-RAY DIFFRACTION100
4.0133-4.32240.15872310.13194755X-RAY DIFFRACTION99
4.3224-4.75590.14982590.12834741X-RAY DIFFRACTION99
4.7559-5.44070.17262570.13634688X-RAY DIFFRACTION99
5.4407-6.8420.19012510.16324750X-RAY DIFFRACTION99
6.842-30.54280.15842460.14254680X-RAY DIFFRACTION96
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)
13.2493-1.2794-2.87954.64430.94253.8485-0.0279-1.49171.00760.19580.04310.01310.05440.1433-0.10030.4249-0.103-0.15260.545-0.05790.461915.813-34.856238.6014
27.006-2.8682-0.75972.0218-0.17820.50280.049-0.31590.06980.0984-0.0338-0.0774-0.02580.1315-0.06610.3245-0.0625-0.12960.3248-0.0410.390920.9225-33.174428.1635
35.8565-1.359-0.43733.23160.8242.484-0.0645-0.7559-0.57370.3905-0.04460.01370.1274-0.05250.08110.4125-0.1149-0.10580.35230.04720.327610.195-37.78435.4878
43.39840.25031.63991.3943-0.64182.69470.1776-0.1235-0.36980.011-0.1427-0.3830.09350.16140.01460.275-0.0326-0.09420.1952-0.00020.410811.5656-37.994123.2058
54.8794-0.10811.26291.70061.51944.0216-0.0699-0.12750.02050.0786-0.05720.65690.3048-0.62480.1020.2469-0.1192-0.00070.2989-0.09370.3389-8.0328-42.252718.8887
62.79960.9565-0.07252.18440.84852.61060.04670.1721-0.65720.0061-0.0376-0.15660.3251-0.0633-0.01550.3233-0.0659-0.06260.2294-0.07180.48343.2828-48.154114.0789
73.88310.09250.09192.54980.86471.6789-0.17520.8902-0.7772-0.34440.4509-0.79210.160.4478-0.16770.3693-0.03540.04410.5577-0.32620.779618.8976-47.75183.4141
82.26322.25841.58532.5440.70313.5958-0.99480.11171.12880.44380.1021.2358-0.753-0.18040.22210.8328-0.0624-0.25240.8872-0.23951.1434-1.2443-45.4072-4.7456
92.64610.7742-0.20845.3472-1.11743.5596-0.22050.5328-0.0816-0.99860.3140.55220.3387-0.4869-0.06050.4491-0.0945-0.15380.350.01010.3506-0.6748-22.7123-3.4687
108.64971.9703-5.73974.0169-4.0555.887-0.15390.40620.4042-0.38160.5292-1.1448-0.2140.9339-0.30080.5871-0.10760.07540.6453-0.07680.619921.767-37.62013.6772
119.5695-4.8747-1.50889.10611.85257.84530.10491.1013-0.3809-0.873-0.17710.8154-0.1342-0.26880.12890.6136-0.1064-0.14590.47570.06940.32123.7703-8.0519-11.8382
127.2395-3.31530.69869.40637.18537.1894-0.09390.388-0.8305-0.6108-0.77981.0657-0.3214-1.02320.81320.46030.026-0.15550.31790.01330.39525.30641.6538-7.689
137.05512.92730.89292.35212.89535.9835-0.37930.8068-0.0087-0.68890.02360.31180.1708-0.02680.29650.47930.0042-0.02030.26470.05240.249911.93710.2483-8.1107
142.56261.54820.33796.5730.49872.55150.0535-0.0440.103-0.2723-0.03340.155-0.2605-0.0037-0.02150.16680.0137-0.03380.17370.03280.129713.42721.10341.0908
154.4224.92251.69087.7871.65833.15780.1259-0.0314-0.21810.2216-0.0471-0.10580.08870.173-0.13390.16850.02930.02220.2046-0.00690.196215.484-5.65026.0342
164.73793.4632-0.17234.71531.67531.51280.2518-0.5130.04390.5927-0.21820.0086-0.18480.0162-0.0720.26750.00340.02350.2450.03580.204211.6017-1.34539.9804
174.90073.62920.07293.0308-0.02173.59820.6437-0.8365-0.32271.4043-1.2118-0.4417-1.51230.3870.32840.6292-0.1587-0.0480.58320.02670.332119.88616.441521.4062
183.51580.1569-0.92898.0792-1.78681.92170.1784-0.48690.75450.5686-0.29060.0786-0.83360.16570.0080.4706-0.06860.03820.3612-0.13630.384514.915914.962712.9862
196.2506-5.7305-5.14545.42764.52785.0805-0.10250.76670.508-0.34370.43681.28060.1267-0.83390.01120.16470.0665-0.01040.40920.14350.8006-9.9737-6.96824.4969
204.2348-0.96440.11716.4024.58024.0056-0.5726-0.06810.54730.5442-0.25342.25210.2862-1.10190.7960.5148-0.0990.07250.48860.1141.0141-14.0842-6.205812.1008
216.8377-0.61220.81367.3964.58916.45820.4348-0.286-0.45340.8603-0.19111.35730.6026-0.9472-0.38360.4102-0.01770.11960.37180.11950.6438-8.1867-12.689713.0507
229.49081.86420.34458.60992.12687.93880.3878-0.5552-0.25930.9084-0.1379-0.40230.58550.0687-0.13240.2886-0.06070.04040.28570.0360.27840.1126-11.69211.7394
236.39261.9042-5.36988.7583-4.49159.5830.818-0.8060.45951.1728-0.54840.8959-0.27930.9935-0.32520.4963-0.03740.17870.3650.0040.5742-2.4278-0.524715.7605
242.84141.017-1.57949.27740.4332.25480.62210.2881.97230.67350.07341.50580.2974-1.0232-0.59970.64710.17840.30210.38550.08431.0732-10.64032.841812.7542
254.3834-4.56363.39165.511-2.23795.4031-0.11620.03081.0111-0.17760.177-0.08790.1124-0.6656-0.05190.2783-0.0076-0.00030.32140.10630.4662-1.8836-5.766.0399
264.68043.2328-5.60093.2878-3.4077.04671.2642-3.1307-1.01790.9257-1.10620.22570.6788-0.43540.06660.491-0.0716-0.14550.4050.14530.439910.9974-8.179613.4946
275.4203-0.3694-2.30523.09220.16352.7701-0.15670.5074-0.4486-0.23530.0725-0.30590.10460.03810.150.4207-0.0482-0.09490.3269-0.08010.347633.6603-20.039758.3022
287.01950.7782-2.72391.1877-0.55421.270.05420.5411-0.24020.0735-0.0849-0.06610.1262-0.21960.07860.3448-0.0378-0.07030.3007-0.02860.188628.5907-9.385861.6009
296.09982.0757-2.08432.6354-0.81522.5880.18790.086-0.57840.1435-0.0017-0.38880.11240.2178-0.08270.43320.0839-0.15190.247-0.08470.354338.8627-17.782363.747
304.91733.4876-1.61313.2263-0.75812.53320.26570.1898-0.17320.3138-0.1117-0.0698-0.2180.0713-0.15650.35670.0054-0.09490.20750.02510.202538.3687-6.051667.3451
314.77330.2664-0.24061.44821.22324.5819-0.12950.1799-0.22640.44120.0664-0.7988-0.06871.1008-0.09120.4526-0.0484-0.19870.47290.02020.409757.8395-3.163372.5876
323.1161-0.16660.74661.0341.04223.39840.213-0.3609-0.17260.3942-0.1211-0.27640.02260.4259-0.08780.4681-0.1272-0.12990.30660.04580.261246.5329-1.04280.165
333.8081-0.3362-0.32932.26560.09034.25460.1304-0.35720.51140.36590.00790.1213-0.65350.0596-0.02580.5913-0.10530.03980.285-0.04120.25630.50748.784184.1325
340.29610.19830.32265.3424-2.511.7377-0.4319-0.85290.9865-0.3998-0.92370.4833-0.80761.45241.20451.0765-0.4355-0.22140.90510.08430.84150.567617.295583.9292
352.11780.3029-0.06255.362-1.90284.67420.0017-0.15230.22960.4336-0.3442-0.4283-0.65960.43020.2160.5219-0.1369-0.08180.35090.05380.273549.88924.278462.1157
363.3353-3.4703-3.50824.13014.83837.21260.02520.5950.88-0.52810.9434-0.3713-0.78790.2129-0.74420.6880.01860.0420.39480.02010.340628.015912.462675.1681
372.97272.3029-2.93755.743-1.93673.60880.0639-0.58960.5955-0.0116-0.07670.2872-0.87531.21710.04880.667-0.1242-0.08320.39150.0170.403445.382136.729151.1166
386.0337-5.9951-3.59846.70715.64098.5302-0.2568-0.18640.5249-0.96690.5457-0.2873-1.31491.2661-0.18010.9-0.3042-0.22890.43990.1440.643644.297236.176240.2603
398.8023-2.78690.03857.60563.86854.1139-0.39490.15610.67650.1774-0.0271-0.0158-1.15730.29330.30770.5842-0.0585-0.06540.34990.07710.285937.418335.992942.0593
403.8019-0.42061.48332.6133-1.22665.49590.07540.5086-0.0356-0.0915-0.0398-0.0255-0.50510.24290.00630.3173-0.0355-0.05420.2614-0.00840.236435.942227.636538.2778
414.47340.46492.70142.3722-0.55144.1490.32920.0794-0.18710.0355-0.22880.13560.3415-0.0666-0.1630.3581-0.0024-0.04410.2692-0.06360.303433.886820.738642.9434
426.7921-0.32072.64932.17420.71476.2520.43160.7597-0.7127-0.1421-0.26760.08010.81690.1168-0.13140.42440.0494-0.04760.3301-0.03220.241737.74118.43537.6615
430.32781.28991.50026.87054.77587.59020.82310.5426-1.4931-1.3359-0.14511.45120.566-0.3561.18910.85610.0401-0.41520.5893-0.20790.776529.416210.218226.5686
443.1945-0.2631-1.19334.13722.89472.61050.54781.96240.0422-1.2124-0.39620.14610.5440.7431-0.03480.7430.2267-0.15650.9697-0.17990.248134.690720.964721.2767
454.2817-6.3144-4.81279.3166.71035.56040.52940.49921.1429-0.30790.1229-1.192-0.3250.7307-0.56520.44950.0018-0.03670.71780.01940.451959.036122.095444.4828
464.6145-4.0121-3.30387.81254.84534.30420.18330.9157-0.1227-0.6662-0.3649-0.87110.07121.73490.43710.51510.1733-0.0490.9697-0.01410.646763.201815.17241.364
472.3244-2.17830.42197.8314-2.53937.9861-0.2278-0.0095-0.4410.5873-0.5053-0.44550.2751.50510.46590.47580.147-0.08140.67830.02990.455557.783712.286847.5888
484.9267-3.98962.9975.7413-4.16063.08980.12770.1806-0.60.63470.14490.16250.29330.4181-0.12430.4886-0.069-0.05020.3715-0.07780.276649.307213.427746.7964
495.1104-4.91620.83764.8479-0.01527.98740.35131.3333-1.5049-0.2977-0.35880.63060.90011.02840.07570.57670.1415-0.00140.6537-0.14170.554351.720113.061535.0518
502.2146-1.4082-2.9958.36741.05544.66490.11511.3165-0.24-0.7571-0.936-0.18860.11340.95430.43380.96210.07210.1261.1508-0.0010.533259.78517.326132.5529
515.6162-1.80310.74445.50480.15563.25930.24890.90280.20610.02670.1175-0.632-0.42510.3035-0.29290.2725-0.0188-0.01250.4839-0.02260.309951.25120.698942.9808
523.8045-1.83142.26447.37920.73942.05430.54570.5634-2.069-0.1211-0.19240.18660.88450.3868-0.37460.68690.1223-0.09040.5281-0.08750.465238.384212.773642.9669
532.33650.2891.80587.62780.75115.93970.388-0.94770.52860.6961-0.0542-0.37070.15520.2121-0.29280.4018-0.0320.06710.4034-0.08580.290132.697316.43182.9706
542.413-0.2803-0.42231.91040.28330.19390.0546-0.717-0.07180.09120.1626-0.03020.07660.0768-0.08710.2568-0.0020.03050.4379-0.00470.154630.36926.04571.04
555.6956-0.24771.68052.21310.30371.09010.0872-0.28350.5508-0.04310.1347-0.3542-0.10120.3679-0.15980.4018-0.05230.14130.4494-0.11860.369939.651715.169-0.5334
563.5869-2.8815-0.63864.1637-0.031.8690.1592-0.28050.0816-0.0596-0.032-0.08140.08850.4628-0.11430.2458-0.04280.05740.34820.0070.196240.58223.5814-4.1811
573.8683-0.557-0.97693.98290.91244.13160.1208-0.46690.7175-0.0731-0.1194-0.9987-0.03831.5714-0.03970.26870.04190.07040.68820.03760.50860.90162.3696-7.5028
583.715-0.4903-0.07452.1706-0.02691.81980.29990.27060.2306-0.6682-0.2506-0.2980.19430.6628-0.09450.4180.1040.09310.49120.08920.255850.4286-0.3514-15.9295
593.7208-0.29890.79353.4175-0.6623.91980.6380.1866-0.5534-0.8878-0.36360.44970.87060.3162-0.18790.81070.2231-0.18750.3663-0.01010.297935.6935-11.3612-21.4298
601.02841.5905-0.50972.2761-0.87740.2353-0.94460.16690.25870.1798-0.8711-1.03890.24921.4241.70391.22990.25110.15661.3614-0.02120.614456.5595-19.5899-18.7781
613.30940.422-1.12414.6754-1.28194.44670.05020.7285-0.2833-0.6222-0.398-0.64150.4750.25360.24440.50160.16410.09640.55550.03670.311854.1233-25.9232.2989
622.7842.5443-0.57957.7293-0.54620.14370.3726-0.4427-0.1943-0.22610.11380.29031.32550.4213-0.16590.9125-0.0227-0.22730.44980.10670.413132.6861-15.5572-12.947
634.0304-3.4227-1.25657.9172-2.90713.5829-0.4233-0.0496-0.8803-1.0551-0.4242-0.77231.231.06560.33570.62450.24540.10430.55810.05620.653849.5876-38.749313.1952
646.93491.14490.47142.47581.62.3936-0.38940.11220.040.27120.3205-1.02670.40531.57750.280.68510.075-0.0660.72140.11240.608847.1503-38.226923.5169
655.7029-1.9283-3.68919.2603-2.90176.73290.09370.1015-0.5832-0.5568-0.23580.08070.98580.04580.15790.29510.0922-0.0760.2767-0.0180.43340.509-38.673421.2148
664.5810.5899-1.30012.9404-1.67251.97670.2848-0.3666-0.19760.0559-0.19290.04470.2256-0.0227-0.06440.2051-0.0127-0.03540.2944-0.00450.260138.4426-30.274424.9866
675.91690.0199-4.98153.0404-1.09816.35260.49420.09260.0816-0.0063-0.28310.396-0.3698-0.2903-0.25210.269-0.0023-0.03860.3199-0.06060.251735.9452-23.620219.7608
687.6697-1.8574-4.0976.14133.16184.91740.4598-0.48770.64730.0594-0.28410.0319-0.40390.146-0.19530.29-0.0592-0.03040.40690.01490.312139.3571-21.087825.4365
690.8188-0.3685-2.55853.4545-1.26149.52710.4319-0.19251.07331.7117-0.07171.5101-1.4289-0.42940.05020.6533-0.07860.31760.4492-0.16910.746829.7474-13.405335.7302
702.8307-1.40340.79468.52891.23642.02160.1425-1.3148-0.09251.40370.02091.1732-0.37710.6266-0.02210.638-0.30790.11650.8619-0.09990.274835.0147-23.923641.5821
713.12850.72063.77753.50651.99615.17740.3128-0.5842-0.66830.1045-0.3438-1.4890.5061.7416-0.93870.1836-0.0119-0.05741.02180.10870.45761.4079-23.033120.3141
720.19280.2798-0.20321.9286-2.0222.4934-0.3877-0.16470.00531.08250.05670.0091-1.01041.6830.37560.6226-0.3072-0.00571.21160.01950.550464.2927-15.792823.7889
737.24520.47381.61864.6244-0.41961.52010.54360.32041.0801-0.075-0.5238-1.0311-1.26351.6506-0.24290.6155-0.32910.10410.94270.120.516259.4208-13.220817.1785
748.26344.7961-5.50239.665-3.60164.26650.55060.00130.0459-0.0765-0.6486-0.1294-1.48870.74240.17710.4657-0.0241-0.02370.5613-0.05640.291551.2156-15.259717.1949
754.4764.04661.29734.06710.74327.31930.5312-1.02310.99230.9838-0.75410.2855-0.98270.40190.20640.5405-0.2042-0.00020.6114-0.070.398252.6722-14.999129.0672
767.31722.41851.61918.35922.52672.57920.9266-2.5969-0.57291.1533-0.9569-1.3552-0.4171.8762-0.15420.7037-0.3242-0.11341.2960.24860.623360.9184-18.317732.3031
776.11252.3458-0.66116.0971.27616.4193-0.0135-0.307-0.6285-0.01520.064-0.1907-0.38640.2671-0.02250.2537-0.04950.01620.48780.00510.23253.4222-22.29321.2514
782.01180.8695-3.2287.29331.62493.2146-0.103-1.21142.4417-0.20510.5706-0.2626-1.8199-0.0266-0.33210.5422-0.06430.07780.5087-0.06690.392940.2064-15.296920.3671
795.9084.85744.96125.96613.16167.1888-0.21891.2755-1.0347-0.19610.4885-0.2025-0.08030.5226-0.12390.45530.1385-0.01470.409-0.03770.320114.61630.735122.7492
803.59691.13350.68640.2429-0.19221.7105-0.03840.2819-0.29120.0532-0.08920.134-0.05180.13430.20260.38090.10420.01480.2445-0.06280.399518.860329.320833.6255
817.00462.14651.3891.38320.61581.7936-0.32210.87210.3947-0.16790.24230.2204-0.1697-0.02680.08950.54360.1477-0.03790.4068-0.00750.33879.168333.89725.4943
824.49211.5151-1.44510.7873-1.0031.93870.07150.0776-0.03090.3327-0.05350.13750.01630.0660.01030.40820.09180.02170.2017-0.03820.36588.70533.347137.8924
831.999-0.2766-0.26661.88920.89363.2299-0.13650.1781-0.06740.2139-0.04470.8767-0.2663-0.62820.09730.37110.13660.0330.2562-0.0420.6046-11.16136.749640.767
842.3307-0.2793-0.52872.06870.70751.76210.0689-0.15070.21010.0973-0.02210.2636-0.08340.0608-0.05780.50590.07480.04280.2323-0.03970.4644-0.60443.412846.274
854.44560.1473-0.72926.68262.82734.8149-0.1201-0.6970.18030.49070.1115-0.1002-0.13680.28860.03680.48390.0649-0.02590.3876-0.04510.402414.399344.340558.0784
865.2343-2.8325-3.15792.44041.29822.6925-0.2754-0.4738-0.33190.78530.45071.0012-0.2223-0.1443-0.36190.87260.15930.13080.76450.10630.84-6.745439.212265.098
871.2853-0.55510.725.4228-2.01892.7229-0.0615-0.41290.16250.81490.39020.8417-0.3978-0.5455-0.32260.57730.13970.17330.37480.00830.5338-4.494817.331663.7624
888.2872-1.30583.53347.8458-5.454.713-0.1833-0.6527-0.85550.7754-0.2213-0.26861.00030.21130.63070.64270.0874-0.03650.52180.06090.466117.64734.145258.2311
896.8391.2668-0.63317.2008-1.28342.3941-0.3485-0.61490.49290.69870.45061.10630.2338-0.4042-0.11530.59240.03220.10040.39770.03830.2769-0.00572.395371.7847
902.5196-0.5403-0.32278.26822.13666.4792-0.39010.30650.7272-0.1218-0.69661.4549-0.291-0.34670.81260.5082-0.0378-0.07550.2905-0.04710.40472.2348-7.036367.9388
916.8158-1.94130.90455.667-1.22187.4205-0.3431-0.41940.10531.0856-0.12330.60140.2169-0.11790.33060.4317-0.09830.0570.26160.06450.23399.0351-4.988869.2018
922.0293-1.40180.51562.8981-0.33632.55480.1825-0.00140.00650.2289-0.028-0.19470.1426-0.0531-0.14410.2689-0.08010.02380.2012-0.00360.199511.3681-5.526660.1773
933.5499-3.3482-1.09464.1030.39662.23310.26020.220.2632-0.3362-0.2068-0.1019-0.13950.1171-0.12070.2947-0.05410.00690.19630.00420.196313.6211.199155.4643
943.6585-1.72350.49843.16180.19031.04790.28310.69720.1499-0.5835-0.13790.0735-0.01790.0968-0.18260.34330.0159-0.00970.23290.03380.187110.2357-3.096351.148
957.2944-3.17061.67432.4788-2.12927.53841.28691.0571-0.1748-1.3515-1.1296-0.58521.63470.730.25420.6370.24090.10790.63370.05320.274819.8473-10.173640.4393
962.2394-0.09820.51613.89460.60752.38440.31350.3503-0.6268-1.0255-0.21230.27771.55840.1935-0.10560.66580.1082-0.12950.3147-0.1380.361514.5436-19.414248.0308
976.43176.35337.21077.07026.60339.3103-0.2213-0.90310.08590.16230.06911.5679-0.1856-1.64690.36390.219-0.062-0.02610.53150.12370.7201-11.83120.778754.6573
987.4063-1.7481-1.35146.66212.94082.59030.36870.5522-0.3685-1.1184-0.18741.510.1768-1.7386-0.12810.52590.0255-0.20790.61340.11750.6991-15.20660.338846.2851
993.6186-1.31592.17226.67053.73526.9640.09310.17660.5734-1.0621-0.25972.1143-0.60330.03040.18780.52670.0182-0.12960.34720.08740.828-9.87137.175946.3492
1004.1423-4.73961.46376.3541.04998.20340.19920.22270.516-0.63660.0287-0.5111-0.4892-0.4562-0.15380.35140.03010.01220.23770.02910.3787-1.6176.669848.4303
1014.3415-3.82225.49375.6554-2.61249.84150.55720.7633-0.2715-0.99220.05370.59190.66540.1089-0.52930.59690.0074-0.06620.40250.01980.4763-2.9409-4.458643.7919
1027.97460.9439-3.80084.20120.98743.87560.5451.2498-1.0948-0.45590.1550.4168-0.2839-0.6532-0.32970.6215-0.0112-0.23150.4708-0.03010.7974-11.1085-8.487645.7387
1035.52944.83-1.17678.464-1.29717.32180.3613-0.04560.14950.11590.12910.8177-0.0716-0.6673-0.47540.35390.0169-0.05550.29840.07090.4127-3.75360.30853.6872
1044.9028-4.002-2.08493.88022.19362.0850.40812.95110.9383-1.5553-0.1611-0.40450.1198-0.2578-0.1740.48340.04680.00810.52350.04250.33759.62543.830147.7081
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 38 THROUGH 61 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 62 THROUGH 91 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 92 THROUGH 133 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 134 THROUGH 175 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 176 THROUGH 204 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 205 THROUGH 265 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 266 THROUGH 339 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 340 THROUGH 352 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 353 THROUGH 427 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 4 THROUGH 12 )
11X-RAY DIFFRACTION11CHAIN C AND (RESID 2 THROUGH 15 )
12X-RAY DIFFRACTION12CHAIN C AND (RESID 16 THROUGH 28 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 29 THROUGH 38 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 39 THROUGH 74 )
15X-RAY DIFFRACTION15CHAIN C AND (RESID 75 THROUGH 98 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 99 THROUGH 120 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 121 THROUGH 130 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 131 THROUGH 147 )
19X-RAY DIFFRACTION19CHAIN D AND (RESID 0 THROUGH 11 )
20X-RAY DIFFRACTION20CHAIN D AND (RESID 12 THROUGH 22 )
21X-RAY DIFFRACTION21CHAIN D AND (RESID 23 THROUGH 34 )
22X-RAY DIFFRACTION22CHAIN D AND (RESID 35 THROUGH 44 )
23X-RAY DIFFRACTION23CHAIN D AND (RESID 45 THROUGH 56 )
24X-RAY DIFFRACTION24CHAIN D AND (RESID 57 THROUGH 65 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 66 THROUGH 71 )
26X-RAY DIFFRACTION26CHAIN D AND (RESID 72 THROUGH 76 )
27X-RAY DIFFRACTION27CHAIN E AND (RESID 38 THROUGH 61 )
28X-RAY DIFFRACTION28CHAIN E AND (RESID 62 THROUGH 91 )
29X-RAY DIFFRACTION29CHAIN E AND (RESID 92 THROUGH 133 )
30X-RAY DIFFRACTION30CHAIN E AND (RESID 134 THROUGH 175 )
31X-RAY DIFFRACTION31CHAIN E AND (RESID 176 THROUGH 204 )
32X-RAY DIFFRACTION32CHAIN E AND (RESID 205 THROUGH 265 )
33X-RAY DIFFRACTION33CHAIN E AND (RESID 266 THROUGH 339 )
34X-RAY DIFFRACTION34CHAIN E AND (RESID 340 THROUGH 352 )
35X-RAY DIFFRACTION35CHAIN E AND (RESID 353 THROUGH 426 )
36X-RAY DIFFRACTION36CHAIN F AND (RESID 5 THROUGH 12 )
37X-RAY DIFFRACTION37CHAIN G AND (RESID 2 THROUGH 15 )
38X-RAY DIFFRACTION38CHAIN G AND (RESID 16 THROUGH 28 )
39X-RAY DIFFRACTION39CHAIN G AND (RESID 29 THROUGH 38 )
40X-RAY DIFFRACTION40CHAIN G AND (RESID 39 THROUGH 74 )
41X-RAY DIFFRACTION41CHAIN G AND (RESID 75 THROUGH 98 )
42X-RAY DIFFRACTION42CHAIN G AND (RESID 99 THROUGH 120 )
43X-RAY DIFFRACTION43CHAIN G AND (RESID 121 THROUGH 130 )
44X-RAY DIFFRACTION44CHAIN G AND (RESID 131 THROUGH 147 )
45X-RAY DIFFRACTION45CHAIN H AND (RESID 0 THROUGH 11 )
46X-RAY DIFFRACTION46CHAIN H AND (RESID 12 THROUGH 22 )
47X-RAY DIFFRACTION47CHAIN H AND (RESID 23 THROUGH 34 )
48X-RAY DIFFRACTION48CHAIN H AND (RESID 35 THROUGH 44 )
49X-RAY DIFFRACTION49CHAIN H AND (RESID 45 THROUGH 56 )
50X-RAY DIFFRACTION50CHAIN H AND (RESID 57 THROUGH 65 )
51X-RAY DIFFRACTION51CHAIN H AND (RESID 66 THROUGH 71 )
52X-RAY DIFFRACTION52CHAIN H AND (RESID 72 THROUGH 76 )
53X-RAY DIFFRACTION53CHAIN I AND (RESID 41 THROUGH 61 )
54X-RAY DIFFRACTION54CHAIN I AND (RESID 62 THROUGH 91 )
55X-RAY DIFFRACTION55CHAIN I AND (RESID 92 THROUGH 133 )
56X-RAY DIFFRACTION56CHAIN I AND (RESID 134 THROUGH 175 )
57X-RAY DIFFRACTION57CHAIN I AND (RESID 176 THROUGH 204 )
58X-RAY DIFFRACTION58CHAIN I AND (RESID 205 THROUGH 265 )
59X-RAY DIFFRACTION59CHAIN I AND (RESID 266 THROUGH 339 )
60X-RAY DIFFRACTION60CHAIN I AND (RESID 340 THROUGH 352 )
61X-RAY DIFFRACTION61CHAIN I AND (RESID 353 THROUGH 426 )
62X-RAY DIFFRACTION62CHAIN J AND (RESID 5 THROUGH 12 )
63X-RAY DIFFRACTION63CHAIN K AND (RESID 2 THROUGH 15 )
64X-RAY DIFFRACTION64CHAIN K AND (RESID 16 THROUGH 28 )
65X-RAY DIFFRACTION65CHAIN K AND (RESID 29 THROUGH 38 )
66X-RAY DIFFRACTION66CHAIN K AND (RESID 39 THROUGH 74 )
67X-RAY DIFFRACTION67CHAIN K AND (RESID 75 THROUGH 98 )
68X-RAY DIFFRACTION68CHAIN K AND (RESID 99 THROUGH 120 )
69X-RAY DIFFRACTION69CHAIN K AND (RESID 121 THROUGH 130 )
70X-RAY DIFFRACTION70CHAIN K AND (RESID 131 THROUGH 147 )
71X-RAY DIFFRACTION71CHAIN L AND (RESID 0 THROUGH 11 )
72X-RAY DIFFRACTION72CHAIN L AND (RESID 12 THROUGH 22 )
73X-RAY DIFFRACTION73CHAIN L AND (RESID 23 THROUGH 34 )
74X-RAY DIFFRACTION74CHAIN L AND (RESID 35 THROUGH 44 )
75X-RAY DIFFRACTION75CHAIN L AND (RESID 45 THROUGH 56 )
76X-RAY DIFFRACTION76CHAIN L AND (RESID 57 THROUGH 65 )
77X-RAY DIFFRACTION77CHAIN L AND (RESID 66 THROUGH 71 )
78X-RAY DIFFRACTION78CHAIN L AND (RESID 72 THROUGH 76 )
79X-RAY DIFFRACTION79CHAIN M AND (RESID 38 THROUGH 61 )
80X-RAY DIFFRACTION80CHAIN M AND (RESID 62 THROUGH 91 )
81X-RAY DIFFRACTION81CHAIN M AND (RESID 92 THROUGH 133 )
82X-RAY DIFFRACTION82CHAIN M AND (RESID 134 THROUGH 175 )
83X-RAY DIFFRACTION83CHAIN M AND (RESID 176 THROUGH 204 )
84X-RAY DIFFRACTION84CHAIN M AND (RESID 205 THROUGH 265 )
85X-RAY DIFFRACTION85CHAIN M AND (RESID 266 THROUGH 339 )
86X-RAY DIFFRACTION86CHAIN M AND (RESID 340 THROUGH 352 )
87X-RAY DIFFRACTION87CHAIN M AND (RESID 353 THROUGH 427 )
88X-RAY DIFFRACTION88CHAIN N AND (RESID 4 THROUGH 12 )
89X-RAY DIFFRACTION89CHAIN O AND (RESID 2 THROUGH 15 )
90X-RAY DIFFRACTION90CHAIN O AND (RESID 16 THROUGH 28 )
91X-RAY DIFFRACTION91CHAIN O AND (RESID 29 THROUGH 38 )
92X-RAY DIFFRACTION92CHAIN O AND (RESID 39 THROUGH 74 )
93X-RAY DIFFRACTION93CHAIN O AND (RESID 75 THROUGH 98 )
94X-RAY DIFFRACTION94CHAIN O AND (RESID 99 THROUGH 120 )
95X-RAY DIFFRACTION95CHAIN O AND (RESID 121 THROUGH 130 )
96X-RAY DIFFRACTION96CHAIN O AND (RESID 131 THROUGH 147 )
97X-RAY DIFFRACTION97CHAIN P AND (RESID 0 THROUGH 11 )
98X-RAY DIFFRACTION98CHAIN P AND (RESID 12 THROUGH 22 )
99X-RAY DIFFRACTION99CHAIN P AND (RESID 23 THROUGH 34 )
100X-RAY DIFFRACTION100CHAIN P AND (RESID 35 THROUGH 44 )
101X-RAY DIFFRACTION101CHAIN P AND (RESID 45 THROUGH 56 )
102X-RAY DIFFRACTION102CHAIN P AND (RESID 57 THROUGH 65 )
103X-RAY DIFFRACTION103CHAIN P AND (RESID 66 THROUGH 71 )
104X-RAY DIFFRACTION104CHAIN P AND (RESID 72 THROUGH 76 )

+
万見について

-
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

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

+
2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る