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- PDB-2xwj: Crystal Structure of Complement C3b in Complex with Factor B -

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基本情報

登録情報
データベース: PDB / ID: 2xwj
タイトルCrystal Structure of Complement C3b in Complex with Factor B
要素
  • (COMPLEMENT C3 ...) x 2
  • COMPLEMENT FACTOR B
キーワードHYDROLASE / IMMUNE SYSTEM / PRO-CONVERTASE / SERINE PROTEASE / CONFORMATIONAL CHANGES / ALTERNATIVE PATHWAY
機能・相同性
機能・相同性情報


alternative-complement-pathway C3/C5 convertase / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement binding / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation ...alternative-complement-pathway C3/C5 convertase / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement binding / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / positive regulation of G protein-coupled receptor signaling pathway / Activation of C3 and C5 / complement receptor mediated signaling pathway / positive regulation of type IIa hypersensitivity / positive regulation of D-glucose transmembrane transport / complement-dependent cytotoxicity / complement activation / complement activation, alternative pathway / endopeptidase inhibitor activity / neuron remodeling / B cell activation / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / complement activation, classical pathway / Peptide ligand-binding receptors / Regulation of Complement cascade / fatty acid metabolic process / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / G alpha (i) signalling events / secretory granule lumen / blood microparticle / receptor ligand activity / inflammatory response / immune response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
類似検索 - 分子機能
Jelly Rolls - #1540 / N-terminal domain of TfIIb - #160 / Complement factor B / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Alpha-macroglobulin, receptor-binding domain / Macroglobulin (MG2) domain / Complement B/C2 / S-adenosyl-L-methionine-dependent methyltransferases / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 ...Jelly Rolls - #1540 / N-terminal domain of TfIIb - #160 / Complement factor B / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Alpha-macroglobulin, receptor-binding domain / Macroglobulin (MG2) domain / Complement B/C2 / S-adenosyl-L-methionine-dependent methyltransferases / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / N-terminal domain of TfIIb / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement Module, domain 1 / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Complement Module; domain 1 / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Glycosyltransferase - #20 / : / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Tissue inhibitor of metalloproteinases-like, OB-fold / von Willebrand factor, type A domain / Other non-globular / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / von Willebrand factor type A domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / Single Sheet / von Willebrand factor A-like domain superfamily / Special / Ribbon / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Jelly Rolls / Immunoglobulins / Peptidase S1, PA clan / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
NICKEL (II) ION / Complement factor B / Complement C3
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: 4 Å
データ登録者Forneris, F. / Ricklin, D. / Wu, J. / Tzekou, A. / Wallace, R.S. / Lambris, J.D. / Gros, P.
引用ジャーナル: Science / 年: 2010
タイトル: Structures of C3B in Complex with Factors B and D Give Insight Into Complement Convertase Formation.
著者: Forneris, F. / Ricklin, D. / Wu, J. / Tzekou, A. / Wallace, R.S. / Lambris, J.D. / Gros, P.
履歴
登録2010年11月4日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02011年1月12日Provider: repository / タイプ: Initial release
改定 1.12012年4月11日Group: Database references / Other ...Database references / Other / Refinement description / Version format compliance
改定 1.22020年7月29日Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
カテゴリ: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 1.32023年12月20日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "II" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "II" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "JH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "KG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "LI" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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: COMPLEMENT C3 BETA CHAIN
B: COMPLEMENT C3 ALPHA CHAIN
C: COMPLEMENT C3 BETA CHAIN
D: COMPLEMENT C3 ALPHA CHAIN
E: COMPLEMENT C3 BETA CHAIN
F: COMPLEMENT C3 ALPHA CHAIN
G: COMPLEMENT C3 BETA CHAIN
H: COMPLEMENT C3 ALPHA CHAIN
I: COMPLEMENT FACTOR B
J: COMPLEMENT FACTOR B
K: COMPLEMENT FACTOR B
L: COMPLEMENT FACTOR B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,036,65424
ポリマ－1,034,64912
非ポリマー2,00412
水1448
1
A: COMPLEMENT C3 BETA CHAIN
B: COMPLEMENT C3 ALPHA CHAIN
I: COMPLEMENT FACTOR B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)259,1636
ポリマ－258,6623
非ポリマー5013
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area16430 Å2
ΔGint-61.5 kcal/mol
Surface area97180 Å2
手法PISA
2
C: COMPLEMENT C3 BETA CHAIN
D: COMPLEMENT C3 ALPHA CHAIN
J: COMPLEMENT FACTOR B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)259,1636
ポリマ－258,6623
非ポリマー5013
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area16600 Å2
ΔGint-59.5 kcal/mol
Surface area97190 Å2
手法PISA
3
G: COMPLEMENT C3 BETA CHAIN
H: COMPLEMENT C3 ALPHA CHAIN
L: COMPLEMENT FACTOR B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)259,1636
ポリマ－258,6623
非ポリマー5013
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area16810 Å2
ΔGint-60 kcal/mol
Surface area96610 Å2
手法PISA
4
E: COMPLEMENT C3 BETA CHAIN
F: COMPLEMENT C3 ALPHA CHAIN
K: COMPLEMENT FACTOR B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)259,1636
ポリマ－258,6623
非ポリマー5013
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area16560 Å2
ΔGint-59.5 kcal/mol
Surface area97370 Å2
手法PISA
単位格子
Length a, b, c (Å)262.160, 297.870, 341.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
13
23
33
43
14
24
34
44
15
25
35
45
16
26
36
46
17
27
37
47
18
28
38
48
19
29
39
49
110
210
310
410
111
211
311
411
112
212
113
213
114
214
314
414
115
215
116
216
117
217
118
218
119
219
120
220
121
221
122
222
123
223
323
423

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:102 )
211CHAIN G AND (RESSEQ 1:102 )
112CHAIN C AND (RESSEQ 1:102 )
212CHAIN E AND (RESSEQ 1:102 )
113CHAIN A AND (RESSEQ 103:650 ) OR CHAIN B AND (RESSEQ 744:804 )
213CHAIN C AND (RESSEQ 103:650 ) OR CHAIN D AND (RESSEQ 744:804 )
313CHAIN E AND (RESSEQ 103:650 ) OR CHAIN F AND (RESSEQ 744:804 )
413CHAIN G AND (RESSEQ 103:650 ) OR CHAIN H AND (RESSEQ 744:804 )
114CHAIN B AND (RESSEQ 805:900 )
214CHAIN D AND (RESSEQ 805:900 )
314CHAIN F AND (RESSEQ 805:900 )
414CHAIN H AND (RESSEQ 805:900 )
115CHAIN B AND (RESSEQ 913:965 OR RESSEQ 1268:1331 )
215CHAIN D AND (RESSEQ 913:965 OR RESSEQ 1268:1331 )
315CHAIN F AND (RESSEQ 913:965 OR RESSEQ 1268:1331 )
415CHAIN H AND (RESSEQ 913:965 OR RESSEQ 1268:1331 )
116CHAIN B AND (RESSEQ 969:1102 )
216CHAIN D AND (RESSEQ 969:1102 )
316CHAIN F AND (RESSEQ 969:1102 )
416CHAIN H AND (RESSEQ 969:1102 )
117CHAIN B AND (RESSEQ 1108:1264 )
217CHAIN D AND (RESSEQ 1108:1264 )
317CHAIN F AND (RESSEQ 1108:1264 )
417CHAIN H AND (RESSEQ 1108:1264 )
118CHAIN B AND (RESSEQ 1332:1480 )
218CHAIN D AND (RESSEQ 1332:1480 )
318CHAIN F AND (RESSEQ 1332:1480 )
418CHAIN H AND (RESSEQ 1332:1480 )
119CHAIN B AND (RESSEQ 1485:1498 )
219CHAIN D AND (RESSEQ 1485:1498 )
319CHAIN F AND (RESSEQ 1485:1498 )
419CHAIN H AND (RESSEQ 1485:1498 )
1110CHAIN B AND (RESSEQ 1500:1531 )
2110CHAIN D AND (RESSEQ 1500:1531 )
3110CHAIN F AND (RESSEQ 1500:1531 )
4110CHAIN H AND (RESSEQ 1500:1531 )
1111CHAIN B AND (RESSEQ 1538:1638 )
2111CHAIN D AND (RESSEQ 1538:1638 )
3111CHAIN F AND (RESSEQ 1538:1638 )
4111CHAIN H AND (RESSEQ 1538:1638 )
1112CHAIN I AND (RESSEQ 10:68 )
2112CHAIN L AND (RESSEQ 10:68 )
1113CHAIN J AND (RESSEQ 10:68 )
2113CHAIN K AND (RESSEQ 10:68 )
1114CHAIN I AND (RESSEQ 78:220 )
2114CHAIN J AND (RESSEQ 78:220 )
3114CHAIN K AND (RESSEQ 78:220 )
4114CHAIN L AND (RESSEQ 78:220 )
1115CHAIN I AND (RESSEQ 244:250 )
2115CHAIN L AND (RESSEQ 244:250 )
1116CHAIN J AND (RESSEQ 244:250 )
2116CHAIN K AND (RESSEQ 244:250 )
1117CHAIN I AND (RESSEQ 260:324 )
2117CHAIN L AND (RESSEQ 260:324 )
1118CHAIN J AND (RESSEQ 260:324 )
2118CHAIN K AND (RESSEQ 260:324 )
1119CHAIN I AND (RESSEQ 330:340 )
2119CHAIN L AND (RESSEQ 330:340 )
1120CHAIN J AND (RESSEQ 330:340 )
2120CHAIN K AND (RESSEQ 330:340 )
1121CHAIN I AND (RESSEQ 360:455 )
2121CHAIN L AND (RESSEQ 360:455 )
1122CHAIN J AND (RESSEQ 360:455 )
2122CHAIN K AND (RESSEQ 360:455 )
1123CHAIN I AND (RESSEQ 485:741 )
2123CHAIN J AND (RESSEQ 485:741 )
3123CHAIN K AND (RESSEQ 485:741 )
4123CHAIN L AND (RESSEQ 485:741 )

NCSアンサンブル:
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23

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要素

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COMPLEMENT C3 ... , 2種, 8分子 ACEGBDFH

#1: タンパク質
COMPLEMENT C3 BETA CHAIN


分子量: 71393.320 Da / 分子数: 4 / 断片: RESIDUES 23-667 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / 器官: BLOOD / 参照: UniProt: P01024
#2: タンパク質
COMPLEMENT C3 ALPHA CHAIN


分子量: 104074.148 Da / 分子数: 4 / 断片: RESIDUES 749-1663 / Mutation: YES / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / 器官: BLOOD / 参照: UniProt: P01024

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タンパク質 / 糖 , 2種, 12分子 IJKL

#3: タンパク質
COMPLEMENT FACTOR B / C3/C5 CONVERTASE / GLYCINE-RICH BETA GLYCOPROTEIN / GBG / PBF2 / PROPERDIN FACTOR B


分子量: 83194.859 Da / 分子数: 4 / 断片: COMPLEMENT FACTOR B / Mutation: YES / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 器官: BLOOD / プラスミド: PUPE.05.05 / 細胞株 (発現宿主): HEK293-ES / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: P00751
#4: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 8 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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非ポリマー , 2種, 12分子

#5: 化合物
ChemComp-NI / NICKEL (II) ION


分子量: 58.693 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Ni
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 8 / 由来タイプ: 天然 / 式: H2O

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詳細

構成要素の詳細ENGINEERED RESIDUE IN CHAIN B, GLN1013 TO GLU ENGINEERED RESIDUE IN CHAIN D, GLN1013 TO GLU ...ENGINEERED RESIDUE IN CHAIN B, GLN1013 TO GLU ENGINEERED RESIDUE IN CHAIN D, GLN1013 TO GLU ENGINEERED RESIDUE IN CHAIN F, GLN1013 TO GLU ENGINEERED RESIDUE IN CHAIN H, GLN1013 TO GLU ENGINEERED RESIDUE IN CHAIN I, ASP 279 TO GLY ENGINEERED RESIDUE IN CHAIN I, ASN 285 TO ASP ENGINEERED RESIDUE IN CHAIN J, ASP 279 TO GLY ENGINEERED RESIDUE IN CHAIN J, ASN 285 TO ASP ENGINEERED RESIDUE IN CHAIN K, ASP 279 TO GLY ENGINEERED RESIDUE IN CHAIN K, ASN 285 TO ASP ENGINEERED RESIDUE IN CHAIN L, ASP 279 TO GLY ENGINEERED RESIDUE IN CHAIN L, ASN 285 TO ASP
配列の詳細MUTANT D254G N260D, PLUS TWO ADDITIONAL ALANINES AT C-TER. RESIDUE 991 FOR CHAINS B,D,F,H HAS BEEN ...MUTANT D254G N260D, PLUS TWO ADDITIONAL ALANINES AT C-TER. RESIDUE 991 FOR CHAINS B,D,F,H HAS BEEN CONVERTED FROM GLN TO GLU IN THE CONVERSION OF C3 TO C3B

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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: 2.78 Å3/Da / 溶媒含有率: 55.7 % / 解説: NONE
結晶化pH: 4 / 詳細: pH 4.0

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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: ESRF / ビームライン: ID14-4 / 波長: 1
検出器タイプ: ADSC CCD / 検出器: CCD / 日付: 2010年3月12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: 4→75 Å / Num. obs: 104810 / % possible obs: 93.4 % / Observed criterion σ(I): 3.5 / 冗長度: 4.3 % / Biso Wilson estimate: 78.22 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.2
反射 シェル解像度: 4→4.22 Å / 冗長度: 4.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.2 / % possible all: 79

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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
iMOSFLMデータ削減
SCALAデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PARTIAL MODEL FROM 2XWB

2xwb


解像度: 4→72.757 Å / SU ML: 0.52 / σ(F): 1.34 / 位相誤差: 29.83 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2808 5237 5 %
Rwork0.2275 --
obs0.2301 104583 93.07 %
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 / Bsol: 59.838 Å2 / ksol: 0.303 e/Å3
原子変位パラメータBiso mean: 126.15 Å2
Baniso -1Baniso -2Baniso -3
1--5.1812 Å20 Å20 Å2
2---48.1353 Å20 Å2
3----13.3221 Å2
精密化ステップサイクル: LAST / 解像度: 4→72.757 Å
タンパク質核酸リガンド溶媒全体
原子数71136 0 116 8 71260
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00172836
X-RAY DIFFRACTIONf_angle_d0.35798559
X-RAY DIFFRACTIONf_dihedral_angle_d7.17326931
X-RAY DIFFRACTIONf_chiral_restr0.02411024
X-RAY DIFFRACTIONf_plane_restr0.00212755
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A771X-RAY DIFFRACTIONPOSITIONAL
12G771X-RAY DIFFRACTIONPOSITIONAL0.091
21C771X-RAY DIFFRACTIONPOSITIONAL
22E771X-RAY DIFFRACTIONPOSITIONAL0.009
31A4709X-RAY DIFFRACTIONPOSITIONAL
32C4709X-RAY DIFFRACTIONPOSITIONAL0.017
33E4709X-RAY DIFFRACTIONPOSITIONAL0.018
34G4709X-RAY DIFFRACTIONPOSITIONAL0.015
41B790X-RAY DIFFRACTIONPOSITIONAL
42D790X-RAY DIFFRACTIONPOSITIONAL0.015
43F790X-RAY DIFFRACTIONPOSITIONAL0.018
44H790X-RAY DIFFRACTIONPOSITIONAL0.008
51B908X-RAY DIFFRACTIONPOSITIONAL
52D908X-RAY DIFFRACTIONPOSITIONAL0.057
53F908X-RAY DIFFRACTIONPOSITIONAL0.052
54H908X-RAY DIFFRACTIONPOSITIONAL0.049
61B1048X-RAY DIFFRACTIONPOSITIONAL
62D1048X-RAY DIFFRACTIONPOSITIONAL0.026
63F1048X-RAY DIFFRACTIONPOSITIONAL0.02
64H1048X-RAY DIFFRACTIONPOSITIONAL0.02
71B1238X-RAY DIFFRACTIONPOSITIONAL
72D1238X-RAY DIFFRACTIONPOSITIONAL0.014
73F1238X-RAY DIFFRACTIONPOSITIONAL0.012
74H1238X-RAY DIFFRACTIONPOSITIONAL0.014
81B1133X-RAY DIFFRACTIONPOSITIONAL
82D1133X-RAY DIFFRACTIONPOSITIONAL0.034
83F1133X-RAY DIFFRACTIONPOSITIONAL0.033
84H1133X-RAY DIFFRACTIONPOSITIONAL0.028
91B115X-RAY DIFFRACTIONPOSITIONAL
92D115X-RAY DIFFRACTIONPOSITIONAL0.03
93F115X-RAY DIFFRACTIONPOSITIONAL0.047
94H115X-RAY DIFFRACTIONPOSITIONAL0.014
101B246X-RAY DIFFRACTIONPOSITIONAL
102D246X-RAY DIFFRACTIONPOSITIONAL0.107
103F246X-RAY DIFFRACTIONPOSITIONAL0.107
104H246X-RAY DIFFRACTIONPOSITIONAL0.106
111B827X-RAY DIFFRACTIONPOSITIONAL
112D827X-RAY DIFFRACTIONPOSITIONAL0.014
113F827X-RAY DIFFRACTIONPOSITIONAL0.015
114H827X-RAY DIFFRACTIONPOSITIONAL0.012
121I453X-RAY DIFFRACTIONPOSITIONAL
122L453X-RAY DIFFRACTIONPOSITIONAL0.009
131J436X-RAY DIFFRACTIONPOSITIONAL
132K436X-RAY DIFFRACTIONPOSITIONAL0.136
141I1115X-RAY DIFFRACTIONPOSITIONAL
142J1115X-RAY DIFFRACTIONPOSITIONAL0.053
143K1115X-RAY DIFFRACTIONPOSITIONAL0.053
144L1115X-RAY DIFFRACTIONPOSITIONAL0.052
151I59X-RAY DIFFRACTIONPOSITIONAL
152L59X-RAY DIFFRACTIONPOSITIONAL0.021
161J59X-RAY DIFFRACTIONPOSITIONAL
162K59X-RAY DIFFRACTIONPOSITIONAL0.011
171I523X-RAY DIFFRACTIONPOSITIONAL
172L523X-RAY DIFFRACTIONPOSITIONAL0.008
181J523X-RAY DIFFRACTIONPOSITIONAL
182K523X-RAY DIFFRACTIONPOSITIONAL0.01
191I85X-RAY DIFFRACTIONPOSITIONAL
192L85X-RAY DIFFRACTIONPOSITIONAL0.01
201J85X-RAY DIFFRACTIONPOSITIONAL
202K85X-RAY DIFFRACTIONPOSITIONAL0.011
211I764X-RAY DIFFRACTIONPOSITIONAL
212L764X-RAY DIFFRACTIONPOSITIONAL0.009
221J764X-RAY DIFFRACTIONPOSITIONAL
222K764X-RAY DIFFRACTIONPOSITIONAL0.083
231I2030X-RAY DIFFRACTIONPOSITIONAL
232J2030X-RAY DIFFRACTIONPOSITIONAL0.009
233K2030X-RAY DIFFRACTIONPOSITIONAL0.01
234L2030X-RAY DIFFRACTIONPOSITIONAL0.008
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.04550.34631310.28622766X-RAY DIFFRACTION77
4.0455-4.0930.30831420.27522789X-RAY DIFFRACTION79
4.093-4.1430.35891450.26342753X-RAY DIFFRACTION78
4.143-4.19540.31391530.25982815X-RAY DIFFRACTION80
4.1954-4.25060.29031540.24272816X-RAY DIFFRACTION80
4.2506-4.30880.31071400.24712888X-RAY DIFFRACTION81
4.3088-4.37040.26791460.23822916X-RAY DIFFRACTION83
4.3704-4.43560.28441680.23043029X-RAY DIFFRACTION85
4.4356-4.50490.28511500.23643064X-RAY DIFFRACTION87
4.5049-4.57870.31221670.22763149X-RAY DIFFRACTION89
4.5787-4.65770.28111620.22683234X-RAY DIFFRACTION92
4.6577-4.74240.26531640.2183367X-RAY DIFFRACTION94
4.7424-4.83360.29691720.20913443X-RAY DIFFRACTION97
4.8336-4.93220.26011820.20623469X-RAY DIFFRACTION98
4.9322-5.03940.25841910.2163464X-RAY DIFFRACTION99
5.0394-5.15660.29381850.20683514X-RAY DIFFRACTION99
5.1566-5.28550.25941980.21043526X-RAY DIFFRACTION100
5.2855-5.42840.25591810.20843546X-RAY DIFFRACTION100
5.4284-5.58810.26451740.22113544X-RAY DIFFRACTION99
5.5881-5.76840.30662030.22223523X-RAY DIFFRACTION100
5.7684-5.97440.30332020.22453546X-RAY DIFFRACTION100
5.9744-6.21350.31881900.22123560X-RAY DIFFRACTION100
6.2135-6.49620.27031880.2273517X-RAY DIFFRACTION100
6.4962-6.83840.29581820.23243585X-RAY DIFFRACTION100
6.8384-7.26650.30731770.2173571X-RAY DIFFRACTION100
7.2665-7.82690.23571870.20133568X-RAY DIFFRACTION100
7.8269-8.61350.22592130.18763567X-RAY DIFFRACTION100
8.6135-9.85720.19651840.17653609X-RAY DIFFRACTION100
9.8572-12.40910.21011990.18293606X-RAY DIFFRACTION99
12.4091-72.76930.35772070.30953602X-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)
10.29850.15160.25570.4901-0.43750.97610.01170.240.0686-0.0432-0.4405-0.1749-0.26550.18630.31850.3520.290.0170.4920.12320.286779.0641-50.9825-12.3543
20.26440.13840.39280.6364-0.3370.53660.01560.15830.1623-0.2197-0.2098-0.40270.1130.45680.33380.27660.34540.21420.52180.32920.4681100.684-49.2548-33.7788
30.9659-0.19560.42091.196-0.76140.4957-0.39430.22970.0058-0.31650.0082-0.24690.260.1930.31310.32360.22320.07590.52030.06680.260684.2614-50.7048-28.3451
41.03920.3953-0.68320.6176-0.52690.77690.19720.2531-0.17-0.4362-0.1803-0.24060.2275-0.3927-0.03550.75770.12380.01510.34010.09470.288164.74-30.3653-54.5326
50.2660.02790.07940.53090.08140.0251-0.1485-0.3583-0.00570.2431-0.28830.0655-0.08670.51260.39991.03230.2440.02130.76990.12960.269267.6876-10.0123-14.4835
60.0643-0.0431-0.0280.07440.09710.17060.0881-0.0501-0.2073-0.26750.145-0.388-0.14810.28250.3627-0.25690.4513-0.4298-0.19910.60910.112486.7805-43.242824.8602
70.49140.30810.42750.89410.5460.5355-0.2041-0.4556-0.0848-0.19650.03870.23670.0563-0.41140.26380.6720.28720.06730.73860.01620.092965.6953-15.743-14.4057
81.90250.4664-0.17880.5003-0.00810.0621-0.3454-0.3738-0.2597-0.3278-0.0203-0.2304-0.15610.11590.22460.39280.05180.0850.31070.13640.228677.5506-6.1388-62.3836
90.7814-0.62970.41480.6217-0.42191.3081-0.23230.19190.07030.0321-0.1085-0.10310.09430.15290.14970.21930.0935-0.09250.2343-0.01720.183737.65928.1842-60.0688
100.44720.2676-0.11920.42520.07240.2102-0.0376-0.0677-0.1122-0.183-0.1710.3569-0.0013-0.06280.16270.1335-0.06010.11730.1988-0.18721.0232152.1216-20.4689-65.6906
110.0937-0.0098-0.15760.21720.0141.07210.2577-0.07450.24830.09020.35780.1158-0.0110.1288-0.53860.0737-0.05180.00190.3416-0.07250.618152.6082-56.2246-54.8602
120.2448-0.2175-0.46430.82560.07730.44780.00380.06120.19990.27170.04150.5440.0181-0.08920.10140.1920.00520.16430.2534-0.14460.8566138.2187-37.4162-36.9194
130.30140.1702-0.30861.91830.05950.5109-0.24670.12270.26760.01630.10731.04180.19110.0850.0325-0.032-0.0315-0.03630.1704-0.04220.4325132.5885-80.2555-46.6951
140.0812-0.08040.13290.80760.28980.4680.1329-0.2093-0.10120.110.1041-0.5042-0.04760.4248-0.10780.1507-0.09930.07410.4270.08820.3899177.0192-71.7956-50.1961
150.42750.4212-0.1160.4038-0.12320.18740.0307-0.1794-0.1562-0.0155-0.0151-0.178-0.06320.30630.01430.20010.00630.23040.3503-0.04380.3391192.3748-23.8333-64.091
161.20180.23570.72850.21510.1810.51880.32420.1187-0.3401-0.18040.0366-0.1736-0.07630.1846-0.2540.12560.12910.11330.61430.06080.4731173.0738-70.6314-54.3403
170.256-0.05250.09681.3467-0.1130.0547-0.1748-0.181-0.12240.73640.19520.01590.1934-0.134-0.00740.5356-0.06730.10830.5703-0.05770.3001140.8412-92.3193-22.4668
180.4652-0.5027-0.43271.2078-0.2981.2164-0.1243-0.0034-0.14840.3032-0.1031-0.0105-0.1506-0.34440.15970.1136-0.0205-0.10410.22650.01920.1271150.6198-123.9547-48.6416
190.60960.33890.23390.47960.15590.11050.0924-0.005-0.05350.1903-0.1511-0.61050.03980.02710.00720.1338-0.1269-0.28870.21450.27090.9225110.9091-39.946861.2661
200.1540.1096-0.02660.50460.00170.2097-0.0594-0.18610.07690.0149-0.275-0.7197-0.09820.01640.27320.38140.014-0.07220.35560.51351.3385119.8014-66.432227.5704
210.47080.42130.23431.1785-0.37161.08370.12890.09580.4792-0.1895-0.535-0.0237-0.04590.32780.30530.3799-0.0267-0.12780.37760.50481.217125.5388-29.982433.2112
220.053-0.00240.13420.01610.03070.33830.06430.18410.21030.09460.1474-0.1453-0.00520.1414-0.15810.0963-0.1461-0.23890.39860.49031.6836129.5344-41.570551.41
230.5282-0.7201-0.00442.0978-0.37140.1242-0.09590.03630.29070.35860.32660.8201-0.04320.0547-0.20020.34440.1822-0.09740.25290.18040.9763113.5471-36.80246.1976
240.20220.0638-0.37160.6755-0.19160.2953-0.20370.07230.26780.1897-0.1143-0.76910.15860.11040.19260.11230.0008-0.17590.26380.29110.9864120.2845-84.091446.6531
251.2912-0.2525-0.06420.7461-0.23570.30410.28390.023-0.2060.3652-0.1672-0.0486-0.0637-0.0045-0.03970.1973-0.0981-0.06860.41540.22870.388370.2718-29.49263.4081
260.73750.1090.17190.9907-0.43760.3687-0.0414-0.20690.2305-0.2344-0.0013-0.18150.2355-0.00210.01290.15310.05010.03220.22310.27360.6402113.3889-94.732432.4994
270.27490.3628-0.06250.5309-0.13420.28880.00410.00830.1387-0.2481-0.03820.18920.10330.27550.00030.1276-0.091-0.12410.45890.26030.5578110.3371-129.28847.2656
280.1832-0.043-0.02290.3939-0.20940.1205-0.1186-0.2220.25210.38790.14590.0822-0.6041-0.2606-0.13241.11340.57310.35970.41820.35030.006351.2331-94.233-13.4427
291.6185-1.0613-0.36751.2281-0.06281.12890.03730.0098-0.2973-0.05970.15940.3991-0.8731-0.8759-0.19790.64740.68030.24590.89650.27190.334231.8108-94.7129-35.8139
300.23990.280.12091.3830.85450.52160.21240.37060.2101-0.16630.6687-0.0733-0.4590.1006-0.67550.85260.3310.29460.765-0.06450.390937.0458-92.7027-18.2648
310.1112-0.119-0.07990.4980.22880.65560.07760.16990.1663-0.34680.19620.1237-0.2324-0.2511-0.21220.82970.08930.21880.40350.07350.158466.3329-113.8353-54.3964
321.1449-0.17340.02640.36430.06130.0080.19770.8148-0.09320.1451-0.1604-0.036-0.5294-0.3098-0.03471.06030.16790.27680.83730.07220.166563.1439-134.7039-14.0261
33-0.0466-0.0138-0.00150.1819-0.29981.4612-0.36230.06480.1176-0.0597-0.15030.0708-0.2401-0.621-0.8885-0.0826-0.02970.4026-0.20230.8105-1.29145.1057-104.675125.6968
341.2660.46310.35322.9445-1.30770.8698-0.015-0.61350.04490.3271-0.1433-0.322-0.6641-0.38790.11440.84460.18670.00190.66480.20360.190866.0153-129.2054-14.3853
352.441-0.09010.02271.1229-0.16840.27620.223-0.5030.0562-0.3157-0.29930.28280.1264-0.08840.03150.4233-0.03850.05090.4323-0.03130.37355.0244-137.963-62.9953
360.51480.4826-0.3351.6890.34991.1549-0.11360.25560.29550.26580.02040.63490.0239-0.184-0.05890.17990.11980.1720.28050.21470.410593.7133-152.0937-59.1545
370.4618-0.0849-0.00880.2567-0.17560.0776-0.05660.2333-0.0838-0.00580.0295-0.07750.39070.09620.00620.41420.0462-0.08280.3161-0.06780.190942.3316-27.4327-49.4428
380.9891-0.6469-0.59861.62240.74610.9279-0.18520.3954-0.33710.20660.03440.53230.4461-0.1578-0.01610.12670.0216-0.07610.22530.10240.161923.008-15.4543-36.2586
390.21680.1074-0.36110.1224-0.06161.5938-0.0366-0.2306-0.24820.09650.0263-0.02690.40480.45660.18060.88850.44830.24590.63480.33490.335141.2639-37.4295-5.5094
401.6453-2.0494-1.04652.68381.3571.793-0.4888-0.1449-0.68460.24460.15940.6972-0.06540.01330.19950.28120.00170.10870.38090.20350.4029125.538-110.8853-65.4836
410.0531-0.06740.0230.53930.28110.3660.0925-0.22230.2865-0.28360.29930.04740.0462-0.185-0.33260.1971-0.1246-0.11050.6347-0.09730.608143.4736-82.3134-65.3801
421.3740.79360.80661.12830.80730.68110.245-0.4677-0.40.4879-0.2367-0.11360.2489-0.4587-0.03430.27620.1085-0.02910.4538-0.00170.0219154.8606-105.7368-79.5243
430.97240.259-0.55411.1103-0.15460.4469-0.040.07020.2534-0.60260.1827-0.2163-0.0348-0.0988-0.09020.42910.05630.27560.20690.02110.2705166.4268-65.9908-87.3892
440.689-1.2203-0.54962.34740.89662.9813-0.681-0.14910.00840.4369-0.1108-0.1109-0.07370.02860.8450.56750.2327-0.05030.2932-0.03481.1911136.3965-116.303565.2369
451.3816-0.74790.75350.4196-0.34850.4026-0.09820.06850.18450.2757-0.0262-0.3933-0.18220.00150.1270.36920.0337-0.33030.36790.32360.9607119.2273-88.075164.7497
460.4516-0.1668-0.05390.1709-0.07590.7132-0.04560.1541-0.20850.0406-0.1180.00250.33180.0364-0.1910.3885-0.1004-0.28340.3140.13370.2295107.3295-111.025279.1887
470.7387-0.24770.07440.18870.12690.42040.0771-0.02680.21530.91980.144-0.05040.05260.0162-0.22510.7930.0887-0.0080.16370.12350.840295.8384-71.170286.2962
480.3975-0.20490.24310.0652-0.150.20860.1728-0.0956-0.06930.0065-0.00770.1206-0.1239-0.3001-0.20.6666-0.09410.1720.47690.1560.305288.4394-116.3766-49.0474
491.01091.0745-1.4391.9695-0.92162.5779-0.36890.2766-0.3125-0.14590.2487-0.50250.5154-0.42760.11420.12940.01980.07150.21330.06270.1784107.5709-128.3525-36.4414
500.4655-0.0794-0.1810.6894-0.1190.05190.0321-0.08610.08810.20680.26240.0287-0.0743-0.0659-0.22510.75890.1418-0.09350.454-0.05410.111288.9334-106.7173-5.3892
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:190)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 191:546)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 547:642)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 730:911)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 912:969)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 970:1262)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 1263:1337)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 1338:1499)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 1500:1641)
10X-RAY DIFFRACTION10(CHAIN C AND RESID 1:103)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 104:204)
12X-RAY DIFFRACTION12(CHAIN C AND RESID 205:642)
13X-RAY DIFFRACTION13(CHAIN D AND RESID 730:914)
14X-RAY DIFFRACTION14(CHAIN D AND RESID 915:968)
15X-RAY DIFFRACTION15(CHAIN D AND RESID 969:1265)
16X-RAY DIFFRACTION16(CHAIN D AND RESID 1266:1336)
17X-RAY DIFFRACTION17(CHAIN D AND RESID 1337:1500)
18X-RAY DIFFRACTION18(CHAIN D AND RESID 1503:1641)
19X-RAY DIFFRACTION19(CHAIN E AND RESID 1:170)
20X-RAY DIFFRACTION20(CHAIN E AND RESID 171:317)
21X-RAY DIFFRACTION21(CHAIN E AND RESID 318:477)
22X-RAY DIFFRACTION22(CHAIN E AND RESID 478:581)
23X-RAY DIFFRACTION23(CHAIN E AND RESID 582:642)
24X-RAY DIFFRACTION24(CHAIN F AND RESID 730:968)
25X-RAY DIFFRACTION25(CHAIN F AND RESID 969:1269)
26X-RAY DIFFRACTION26(CHAIN F AND RESID 1270:1518)
27X-RAY DIFFRACTION27(CHAIN F AND RESID 1519:1641)
28X-RAY DIFFRACTION28(CHAIN G AND RESID 1:204)
29X-RAY DIFFRACTION29(CHAIN G AND RESID 205:580)
30X-RAY DIFFRACTION30(CHAIN G AND RESID 581:642)
31X-RAY DIFFRACTION31(CHAIN H AND RESID 730:914)
32X-RAY DIFFRACTION32(CHAIN H AND RESID 915:968)
33X-RAY DIFFRACTION33(CHAIN H AND RESID 969:1266)
34X-RAY DIFFRACTION34(CHAIN H AND RESID 1267:1334)
35X-RAY DIFFRACTION35(CHAIN H AND RESID 1335:1505)
36X-RAY DIFFRACTION36(CHAIN H AND RESID 1506:1641)
37X-RAY DIFFRACTION37(CHAIN I AND RESID 10:197)
38X-RAY DIFFRACTION38(CHAIN I AND RESID 198:454)
39X-RAY DIFFRACTION39(CHAIN I AND RESID 455:741)
40X-RAY DIFFRACTION40(CHAIN J AND RESID 10:74)
41X-RAY DIFFRACTION41(CHAIN J AND RESID 75:193)
42X-RAY DIFFRACTION42(CHAIN J AND RESID 194:450)
43X-RAY DIFFRACTION43(CHAIN J AND RESID 451:741)
44X-RAY DIFFRACTION44(CHAIN K AND RESID 10:74)
45X-RAY DIFFRACTION45(CHAIN K AND RESID 75:196)
46X-RAY DIFFRACTION46(CHAIN K AND RESID 197:450)
47X-RAY DIFFRACTION47(CHAIN K AND RESID 451:741)
48X-RAY DIFFRACTION48(CHAIN L AND RESID 10:192)
49X-RAY DIFFRACTION49(CHAIN L AND RESID 193:446)
50X-RAY DIFFRACTION50(CHAIN L AND RESID 447:741)

+
万見について

-
お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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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