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- PDB-2win: C3 convertase (C3bBb) stabilized by SCIN -

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基本情報

登録情報
データベース: PDB / ID: 2win
タイトルC3 convertase (C3bBb) stabilized by SCIN
要素
  • COMPLEMENT C3 BETA CHAIN
  • COMPLEMENT C3B ALPHA' CHAIN
  • COMPLEMENT FACTOR B
  • STAPHYLOCOCCAL COMPLEMENT INHIBITOR
キーワードIMMUNE SYSTEM / SERINE PROTEASE / IMMUNE RESPONSE / INNATE IMMUNITY / ZYMOGEN / SECRETED / PROTEASE / GLYCATION / ALTERNATIVE PATHWAY / DISEASE MUTATION / HYDROLASE / CONVERTASE / COMPLEMENT / POLYMORPHISM / IMMUNE EVASION
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 / Activation of C3 and C5 / positive regulation of phagocytosis, engulfment / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / complement receptor mediated signaling pathway / positive regulation of type IIa hypersensitivity / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / complement activation / complement activation, alternative pathway / endopeptidase inhibitor activity / neuron remodeling / amyloid-beta clearance / B cell activation / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / Purinergic signaling in leishmaniasis infection / 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) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of angiogenesis / azurophil granule lumen / positive regulation of protein phosphorylation / G alpha (i) signalling events / secretory granule lumen / blood microparticle / immune response / G protein-coupled receptor signaling pathway / inflammatory response / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / 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
Staphylococcal complement inhibitor SCIN / Staphylococcal complement inhibitor SCIN / Jelly Rolls - #1540 / N-terminal domain of TfIIb - #160 / Complement factor B / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Alpha-macroglobulin, receptor-binding domain / Complement B/C2 / S-adenosyl-L-methionine-dependent methyltransferases / Macroglobulin (MG2) domain ...Staphylococcal complement inhibitor SCIN / Staphylococcal complement inhibitor SCIN / Jelly Rolls - #1540 / N-terminal domain of TfIIb - #160 / Complement factor B / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Alpha-macroglobulin, receptor-binding domain / Complement B/C2 / S-adenosyl-L-methionine-dependent methyltransferases / Macroglobulin (MG2) domain / Immunoglobulin-like - #1940 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / N-terminal domain of TfIIb / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / : / Anaphylatoxin domain signature. / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Glycosyltransferase - #20 / Netrin domain / NTR domain profile. / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Tissue inhibitor of metalloproteinases-like, OB-fold / 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 / von Willebrand factor, type A domain / Other non-globular / Sushi repeat (SCR repeat) / Heat shock protein 70kD, C-terminal domain superfamily / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / von Willebrand factor type A domain / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Jelly Rolls / Immunoglobulin-like fold / Peptidase S1, PA clan / Immunoglobulins / Up-down Bundle / Beta Barrel / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
beta-D-mannopyranose / alpha-D-mannopyranose / Complement factor B / Complement C3 / Staphylococcal complement inhibitor
類似検索 - 構成要素
生物種HOMO SAPIENS (ヒト)
STAPHYLOCOCCUS AUREUS (黄色ブドウ球菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.9 Å
データ登録者Wu, J. / Janssen, B.J. / Gros, P.
引用ジャーナル: Nat. Immunol. / 年: 2009
タイトル: Structural and functional implications of the alternative complement pathway C3 convertase stabilized by a staphylococcal inhibitor.
著者: Rooijakkers, S.H. / Wu, J. / Ruyken, M. / van Domselaar, R. / Planken, K.L. / Tzekou, A. / Ricklin, D. / Lambris, J.D. / Janssen, B.J. / van Strijp, J.A. / Gros, P.
履歴
登録2009年5月13日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02009年6月9日Provider: repository / タイプ: Initial release
改定 1.12011年5月8日Group: Version format compliance
改定 1.22011年7月13日Group: Version format compliance
改定 1.32018年1月17日Group: Advisory / Database references / Source and taxonomy
カテゴリ: citation / citation_author ...citation / citation_author / entity_src_gen / pdbx_unobs_or_zero_occ_residues
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_strain
改定 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.12023年12月13日Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "JB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "KB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "LB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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 C3B ALPHA' CHAIN
C: COMPLEMENT C3 BETA CHAIN
D: COMPLEMENT C3B ALPHA' CHAIN
E: COMPLEMENT C3 BETA CHAIN
F: COMPLEMENT C3B ALPHA' CHAIN
G: COMPLEMENT C3 BETA CHAIN
H: COMPLEMENT C3B ALPHA' CHAIN
I: COMPLEMENT FACTOR B
J: COMPLEMENT FACTOR B
K: COMPLEMENT FACTOR B
L: COMPLEMENT FACTOR B
M: STAPHYLOCOCCAL COMPLEMENT INHIBITOR
N: STAPHYLOCOCCAL COMPLEMENT INHIBITOR
P: STAPHYLOCOCCAL COMPLEMENT INHIBITOR
Q: STAPHYLOCOCCAL COMPLEMENT INHIBITOR
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)984,82938
ポリマ－974,01616
非ポリマー10,81322
水1448
1
A: COMPLEMENT C3 BETA CHAIN
B: COMPLEMENT C3B ALPHA' CHAIN
G: COMPLEMENT C3 BETA CHAIN
H: COMPLEMENT C3B ALPHA' CHAIN
J: COMPLEMENT FACTOR B
L: COMPLEMENT FACTOR B
N: STAPHYLOCOCCAL COMPLEMENT INHIBITOR
Q: STAPHYLOCOCCAL COMPLEMENT INHIBITOR
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)491,96819
ポリマ－487,0088
非ポリマー4,96011
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area38830 Å2
ΔGint-227.2 kcal/mol
Surface area238000 Å2
手法PQS
2
C: COMPLEMENT C3 BETA CHAIN
D: COMPLEMENT C3B ALPHA' CHAIN
E: COMPLEMENT C3 BETA CHAIN
F: COMPLEMENT C3B ALPHA' CHAIN
I: COMPLEMENT FACTOR B
K: COMPLEMENT FACTOR B
M: STAPHYLOCOCCAL COMPLEMENT INHIBITOR
P: STAPHYLOCOCCAL COMPLEMENT INHIBITOR
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)492,86119
ポリマ－487,0088
非ポリマー5,85311
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area40640 Å2
ΔGint-236.7 kcal/mol
Surface area236850 Å2
手法PQS
単位格子
Length a, b, c (Å)228.632, 121.491, 280.783
Angle α, β, γ (deg.)90.00, 91.64, 90.00
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
12
22
32
42
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
111
211
112
212
312
113
213
114
214
115
215
315
415
116
216
316
416
117
217
317
417
118
218
119
219
120
220
320
420

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:72 OR RESSEQ 78: 104 )
211CHAIN E AND (RESSEQ 1:72 OR RESSEQ 78: 104 )
311CHAIN C AND (RESSEQ 1:72 OR RESSEQ 78: 104 )
411CHAIN G AND (RESSEQ 1:72 OR RESSEQ 78: 104 )
112CHAIN A AND (RESSEQ 105:209 )
212CHAIN E AND (RESSEQ 105:209 )
312CHAIN C AND (RESSEQ 105:209 )
412CHAIN G AND (RESSEQ 105:209 )
113CHAIN A AND (RESSEQ 210:289 )
213CHAIN E AND (RESSEQ 210:289 )
313CHAIN C AND (RESSEQ 210:289 )
413CHAIN G AND (RESSEQ 210:289 )
114CHAIN A AND (RESSEQ 297:328 )
214CHAIN E AND (RESSEQ 297:328 )
314CHAIN C AND (RESSEQ 297:328 )
414CHAIN G AND (RESSEQ 297:328 )
115CHAIN A AND (RESSEQ 329:369 )
215CHAIN E AND (RESSEQ 329:369 )
315CHAIN C AND (RESSEQ 329:369 )
415CHAIN G AND (RESSEQ 329:369 )
116CHAIN A AND (RESSEQ 377:426 )
216CHAIN E AND (RESSEQ 377:426 )
316CHAIN C AND (RESSEQ 377:426 )
416CHAIN G AND (RESSEQ 377:426 )
117CHAIN A AND (RESSEQ 427:485 OR RESSEQ 492:534 )
217CHAIN E AND (RESSEQ 427:485 OR RESSEQ 492:534 )
317CHAIN C AND (RESSEQ 427:485 OR RESSEQ 492:534 )
417CHAIN G AND (RESSEQ 427:485 OR RESSEQ 492:534 )
118CHAIN A AND (RESSEQ 535:642 )
218CHAIN E AND (RESSEQ 535:642 )
318CHAIN C AND (RESSEQ 535:642 )
418CHAIN G AND (RESSEQ 535:642 )
119CHAIN B AND (RESSEQ 746:806 )
219CHAIN F AND (RESSEQ 746:806 )
319CHAIN D AND (RESSEQ 746:806 )
419CHAIN H AND (RESSEQ 746:806 )
1110CHAIN F AND (RESSEQ 1331:1349 OR RESSEQ 1359:1480 )
2110CHAIN H AND (RESSEQ 1331:1349 OR RESSEQ 1359:1480 )
1111CHAIN B AND (RESSEQ 1331:1351 OR RESSEQ 1358:1480 )
2111CHAIN D AND (RESSEQ 1331:1349 OR RESSEQ 1356:1480 )
1112CHAIN B AND (RESSEQ 971:1041 OR RESSEQ 1046:1262 )
2112CHAIN D AND (RESSEQ 971:1041 OR RESSEQ 1046:1262 )
3112CHAIN F AND (RESSEQ 971:1041 OR RESSEQ 1046:1262 )
1113CHAIN B AND (RESSEQ 1481:1498 OR RESSEQ 1501:1637 )
2113CHAIN D AND (RESSEQ 1481:1498 OR RESSEQ 1501:1637 )
1114CHAIN F AND (RESSEQ 1505:1636 )
2114CHAIN H AND (RESSEQ 1505:1636 )
1115CHAIN L AND (RESSEQ 235:449 )
2115CHAIN J AND (RESSEQ 235:449 )
3115CHAIN K AND (RESSEQ 235:449 )
4115CHAIN I AND (RESSEQ 235:449 )
1116CHAIN L AND (RESSEQ 450:741 )
2116CHAIN J AND (RESSEQ 450:741 )
3116CHAIN K AND (RESSEQ 450:741 )
4116CHAIN I AND (RESSEQ 450:741 )
1117CHAIN M AND (RESSEQ 2:85 )
2117CHAIN N AND (RESSEQ 2:85 )
3117CHAIN P AND (RESSEQ 2:85 )
4117CHAIN Q AND (RESSEQ 2:85 )
1118CHAIN B AND (RESSEQ 915:963 OR RESSEQ 1271:1330 )
2118CHAIN D AND (RESSEQ 915:963 OR RESSEQ 1271:1330 )
1119CHAIN F AND (RESSEQ 915:963 OR RESSEQ 1271:1330 )
2119CHAIN H AND (RESSEQ 915:963 OR RESSEQ 1271:1330 )
1120CHAIN B AND (RESSEQ 729:745 OR RESSEQ 807:911 )
2120CHAIN F AND (RESSEQ 729:745 OR RESSEQ 807:911 )
3120CHAIN D AND (RESSEQ 729:745 OR RESSEQ 807:911 )
4120CHAIN H AND (RESSEQ 729:745 OR RESSEQ 807:911 )

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

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要素

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タンパク質 , 4種, 16分子 ACEGBDFHIJKLMNPQ

#1: タンパク質
COMPLEMENT C3 BETA CHAIN


分子量: 71393.320 Da / 分子数: 4 / 断片: COMPLEMENT C3B BETA CHAIN, RESIDUES 23-667 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / 参照: UniProt: P01024
#2: タンパク質
COMPLEMENT C3B ALPHA' CHAIN


分子量: 104073.164 Da / 分子数: 4 / 断片: COMPLEMENT C3B ALPHA' CHAIN, RESIDUES 749-1663 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / 参照: UniProt: P01024
#3: タンパク質
COMPLEMENT FACTOR B


分子量: 57258.277 Da / 分子数: 4 / 断片: COMPLEMENT FACTOR B BB FRAGMENT, RESIDUES 260-764 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PUPE06.08-FBWT / 細胞株 (発現宿主): HEK293ES / 発現宿主: HOMO SAPIENS (ヒト) / Variant (発現宿主): GNTI-
参照: UniProt: P00751, alternative-complement-pathway C3/C5 convertase
#4: タンパク質
STAPHYLOCOCCAL COMPLEMENT INHIBITOR


分子量: 10779.215 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) STAPHYLOCOCCUS AUREUS (黄色ブドウ球菌)
プラスミド: PRSETB / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q6GFB4

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糖 , 11種, 18分子

#5: 多糖
beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 748.682 Da / 分子数: 4 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 多糖 beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-3DManpb1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2/a4-b1_b4-c1_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE
#7: 多糖 beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)-beta-D- ...beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1072.964 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-3[DManpb1-6]DManpb1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2-2/a4-b1_b4-c1_c6-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE
#8: 多糖 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 748.682 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#9: 多糖 alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 586.542 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#10: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#11: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#12: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 586.542 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#13: 糖 ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / β-D-マンノピラノ-ス


タイプ: D-saccharide, beta linking / 分子量: 180.156 Da / 分子数: 2 / 由来タイプ: 組換発現 / 式: C6H12O6
識別子タイププログラム
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#14: 糖 ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / α-D-マンノピラノ-ス


タイプ: D-saccharide, alpha linking / 分子量: 180.156 Da / 分子数: 1 / 由来タイプ: 組換発現 / 式: C6H12O6
識別子タイププログラム
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#16: 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: 2 / 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

-
非ポリマー , 2種, 12分子

#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: 4 / 由来タイプ: 合成 / 式: Mg
#17: 水 ChemComp-HOH / water


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

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.1 Å3/Da / 溶媒含有率: 68 % / 解説: NONE
結晶化pH: 6.5
詳細: 75 MM SODIUM/POTASSIUM TARTRATE, 8.0% PEG 3350, 50 MM BIS-TRIS PROPANE, PH 6.5

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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: 0.975
検出器タイプ: ADSC CCD / 検出器: CCD / 日付: 2008年3月2日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.975 Å / 相対比: 1
反射解像度: 3.9→40 Å / Num. obs: 137476 / % possible obs: 97.6 % / Observed criterion σ(I): -3.7 / 冗長度: 3.5 % / Biso Wilson estimate: 125.23 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.4
反射 シェル解像度: 3.9→4.1 Å / 冗長度: 3.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.8 / % possible all: 92

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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
MOSFLM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: PDB ENTRIES 2A74, 2I07,1RRK, 2QFF

2a74

2i07

1rrk

2qff


解像度: 3.9→39.675 Å / SU ML: 0.57 / σ(F): 1.34 / 位相誤差: 26.44 / 立体化学のターゲット値: ML
詳細: OCCUPANCY OF RESIDUES 968-1267 OF CHAIN H ARE SET TO 0.00
Rfactor反射数%反射
Rfree0.2679 2088 1.5 %
Rwork0.2531 --
obs0.2533 137444 97.63 %
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: 69.409 Å2 / ksol: 0.295 e/Å3
原子変位パラメータBiso mean: 158.8 Å2
Baniso -1Baniso -2Baniso -3
1--8.266 Å20 Å2-4.9722 Å2
2---10.927 Å2-0 Å2
3---19.193 Å2
精密化ステップサイクル: LAST / 解像度: 3.9→39.675 Å
タンパク質核酸リガンド溶媒全体
原子数67266 0 715 8 67989
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00269445
X-RAY DIFFRACTIONf_angle_d0.51994103
X-RAY DIFFRACTIONf_dihedral_angle_d14.37925971
X-RAY DIFFRACTIONf_chiral_restr0.03410771
X-RAY DIFFRACTIONf_plane_restr0.00212013
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A759X-RAY DIFFRACTIONPOSITIONAL
12E759X-RAY DIFFRACTIONPOSITIONAL0.005
13C759X-RAY DIFFRACTIONPOSITIONAL0.003
14G759X-RAY DIFFRACTIONPOSITIONAL0.008
21A847X-RAY DIFFRACTIONPOSITIONAL
22E847X-RAY DIFFRACTIONPOSITIONAL0.005
23C847X-RAY DIFFRACTIONPOSITIONAL0.003
24G847X-RAY DIFFRACTIONPOSITIONAL0.008
31A636X-RAY DIFFRACTIONPOSITIONAL
32E636X-RAY DIFFRACTIONPOSITIONAL0.004
33C636X-RAY DIFFRACTIONPOSITIONAL0.001
34G636X-RAY DIFFRACTIONPOSITIONAL0.005
41A232X-RAY DIFFRACTIONPOSITIONAL
42E232X-RAY DIFFRACTIONPOSITIONAL0.008
43C232X-RAY DIFFRACTIONPOSITIONAL0.002
44G232X-RAY DIFFRACTIONPOSITIONAL0.011
51A328X-RAY DIFFRACTIONPOSITIONAL
52E328X-RAY DIFFRACTIONPOSITIONAL0.007
53C328X-RAY DIFFRACTIONPOSITIONAL0.001
54G328X-RAY DIFFRACTIONPOSITIONAL0.01
61A380X-RAY DIFFRACTIONPOSITIONAL
62E380X-RAY DIFFRACTIONPOSITIONAL0.006
63C380X-RAY DIFFRACTIONPOSITIONAL0.003
64G380X-RAY DIFFRACTIONPOSITIONAL0.01
71A817X-RAY DIFFRACTIONPOSITIONAL
72E817X-RAY DIFFRACTIONPOSITIONAL0.007
73C817X-RAY DIFFRACTIONPOSITIONAL0.004
74G817X-RAY DIFFRACTIONPOSITIONAL0.018
81A799X-RAY DIFFRACTIONPOSITIONAL
82E799X-RAY DIFFRACTIONPOSITIONAL0.006
83C799X-RAY DIFFRACTIONPOSITIONAL0.004
84G799X-RAY DIFFRACTIONPOSITIONAL0.019
91B485X-RAY DIFFRACTIONPOSITIONAL
92F485X-RAY DIFFRACTIONPOSITIONAL0.005
93D485X-RAY DIFFRACTIONPOSITIONAL0.002
94H485X-RAY DIFFRACTIONPOSITIONAL0.007
101F1142X-RAY DIFFRACTIONPOSITIONAL
102H1142X-RAY DIFFRACTIONPOSITIONAL0.007
111B1143X-RAY DIFFRACTIONPOSITIONAL
112D1143X-RAY DIFFRACTIONPOSITIONAL0.023
121B2267X-RAY DIFFRACTIONPOSITIONAL
122D2267X-RAY DIFFRACTIONPOSITIONAL0.003
123F2267X-RAY DIFFRACTIONPOSITIONAL0.002
131B1260X-RAY DIFFRACTIONPOSITIONAL
132D1260X-RAY DIFFRACTIONPOSITIONAL0.007
141F1081X-RAY DIFFRACTIONPOSITIONAL
142H1081X-RAY DIFFRACTIONPOSITIONAL0.003
151L1694X-RAY DIFFRACTIONPOSITIONAL
152J1694X-RAY DIFFRACTIONPOSITIONAL0.007
153K1694X-RAY DIFFRACTIONPOSITIONAL0.008
154I1694X-RAY DIFFRACTIONPOSITIONAL0.003
161L2310X-RAY DIFFRACTIONPOSITIONAL
162J2310X-RAY DIFFRACTIONPOSITIONAL0.004
163K2310X-RAY DIFFRACTIONPOSITIONAL0.004
164I2310X-RAY DIFFRACTIONPOSITIONAL0.002
171M682X-RAY DIFFRACTIONPOSITIONAL
172N682X-RAY DIFFRACTIONPOSITIONAL0.001
173P682X-RAY DIFFRACTIONPOSITIONAL0.001
174Q682X-RAY DIFFRACTIONPOSITIONAL0.001
181B847X-RAY DIFFRACTIONPOSITIONAL
182D847X-RAY DIFFRACTIONPOSITIONAL0.007
191F847X-RAY DIFFRACTIONPOSITIONAL
192H847X-RAY DIFFRACTIONPOSITIONAL0.011
201B986X-RAY DIFFRACTIONPOSITIONAL
202F986X-RAY DIFFRACTIONPOSITIONAL0.005
203D986X-RAY DIFFRACTIONPOSITIONAL0.004
204H986X-RAY DIFFRACTIONPOSITIONAL0.005
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-3.99070.34761320.33788356X-RAY DIFFRACTION91
3.9907-4.09040.33371300.32328440X-RAY DIFFRACTION92
4.0904-4.20080.28921250.30768671X-RAY DIFFRACTION94
4.2008-4.32430.31271370.29128738X-RAY DIFFRACTION95
4.3243-4.46370.2771290.26958929X-RAY DIFFRACTION97
4.4637-4.6230.25361390.25819034X-RAY DIFFRACTION99
4.623-4.80780.27371370.25129103X-RAY DIFFRACTION99
4.8078-5.02620.2371240.24469239X-RAY DIFFRACTION100
5.0262-5.29060.27461350.24189202X-RAY DIFFRACTION100
5.2906-5.62120.26991680.24679171X-RAY DIFFRACTION100
5.6212-6.05390.28241320.26219238X-RAY DIFFRACTION100
6.0539-6.66050.29811410.26029262X-RAY DIFFRACTION100
6.6605-7.61840.27991660.24699261X-RAY DIFFRACTION100
7.6184-9.5760.22411350.20499311X-RAY DIFFRACTION100
9.576-39.67730.21831580.21619401X-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)
11.54641.76210.10213.19530.92172.68390.16080.06250.1212-0.25170.0223-0.253-0.9798-0.0571-01.28580.1784-0.09641.44620.13591.3959117.05224.9421122.6966
21.70230.7532-0.65794.79180.82634.438-0.7430.1161-0.05820.58950.1076-0.1188-1.29060.6135-01.76930.23730.08621.5508-0.12171.2722.490697.263538.622
32.98641.761-1.94364.54660.02433.7197-0.17980.0772-0.8639-0.3436-0.01160.32771.1576-0.08-01.0550.3776-0.05611.28420.03590.932-7.057266.2038-17.7124
4-1.2970.757-0.31174.0501-0.092.319-0.76820.1069-0.54880.64150.0666-0.63951.2068-0.2716-0.00022.17130.226-0.48531.9184-0.15422.253887.0796-5.7896180.0393
53.80821.4175-0.42984.03690.78515.3290.06730.7354-0.2366-0.4414-0.0906-0.53770.22710.49350.00031.04010.1323-0.19380.99220.08021.01982.705928.6367106.957
64.26110.9621.6375.1971-1.26564.8515-0.2191-0.94950.17520.78160.3324-0.0374-0.7683-0.096-0.00021.09120.0480.15121.2387-0.14250.930951.582572.542836.9076
74.48221.65430.08764.72291.41865.69230.19170.92940.059-0.4208-0.30320.4396-0.1887-0.72510.00020.91130.31060.14670.9360.11550.717327.242362.75-33.8021
83.671.0032-0.54953.12330.44054.2855-0.387-0.7976-0.17341.15190.3714-0.8490.47650.3647-0.00041.36260.0255-0.20961.29570.22011.078758.081419.2852178.1859
93.6742-2.3195-0.7118.57990.30771.0238-0.15490.085-0.2711-0.0868-0.08-0.36810.3574-0.21870.00011.2634-0.2376-0.22890.8833-0.01011.167361.4413.7216119.9884
107.56623.9501-3.02126.5623-0.490.91870.29280.41-0.20830.1741-0.14140.4166-0.273-0.2328-0.00010.76010.014-0.08680.94310.15220.751340.177842.672721.7879
112.0295-1.67830.91558.4357-0.53252.39740.0821-0.10730.2349-0.5425-0.0091-0.3038-0.3608-0.12320.00031.1778-0.00420.32130.85670.16531.149648.501287.8521-21.143
125.17735.01293.24677.04442.19432.60520.2390.1184-0.04540.2851-0.1903-0.76560.51010.1914-0.00020.978-0.12820.00921.06870.06991.205469.896349.0158162.9193
133.13932.2233-0.59232.5308-0.15612.1390.0422-0.7339-0.72511.1501-0.44480.1107-0.28010.4827-0.00011.8012-0.0329-0.2081.17810.10081.409790.6351-0.8113138.2199
141.11640.0975-1.58814.56570.68370.8945-0.13910.0258-0.3351-0.72610.10240.5242-0.527-0.7287-0.00021.24170.0483-0.03741.47510.2231.554912.81463.447919.0067
154.76853.0159-0.03290.98840.43161.54840.0579-0.830.37370.22940.036-0.6808-0.1657-0.0037-0.00011.34620.16430.05311.01320.09241.054119.640192.0545-2.4626
16-1.9626-1.4598-2.13180.9006-0.5198-0.9798-0.43250.5469-0.05070.0026-0.1179-2.51270.74560.37960.00011.7232-0.12030.11331.9561-0.22993.574897.312527.8222160.4619
172.6843-0.2356-0.39383.1206-0.82431.8003-0.0318-1.2732-0.72510.5771-0.0276-0.20020.0354-0.4106-0.00021.29560.1615-0.41381.42790.3571.2446107.632915.0783141.1012
183.64250.95252.45714.2058-0.89444.31690.3990.67330.237-0.5544-0.10240.3363-0.3666-0.3824-01.23520.31990.19231.44170.12731.219412.988487.248720.3874
195.6041-0.45151.79895.96250.32777.8588-0.4256-1.25760.43520.40890.6038-0.13060.24660.47380.00020.96560.30560.12590.9758-0.01720.48062.537675.95710.654
200.6360.1476-1.2219-2.5723-0.01580.58190.19990.45330.32210.0114-0.0314-1.3749-0.08230.52330.00171.56780.3435-0.08842.12470.03473.08796.87714.2796162.1222
218.40460.79210.63963.9227-0.17332.3647-0.0863-0.84990.33840.3199-0.00750.2028-0.63680.0173-0.00031.0551-0.0664-0.1570.7793-0.00090.929672.372937.5812125.6686
225.044-2.6501-0.00496.2110.40163.260.2140.32640.47450.01560.0344-0.4808-0.5452-0.1023-0.00021.1152-0.15730.23351.11190.08740.794855.334274.75614.1863
238.6868-0.1153-1.40163.81860.95772.8214-0.0236-0.7894-0.7253-0.0727-0.1656-0.16570.2684-0.1622-0.00020.91480.10670.14040.81440.18690.718637.813953.8105-15.2087
243.4664-3.75010.50025.7010.37411.45860.17440.3697-0.6659-0.22420.01620.33040.54310.33930.00021.2609-0.1593-0.12321.21590.02281.158954.674317.0213155.4373
253.70910.2327-0.05273.829-1.14926.52240.18250.25690.12950.0331-0.07210.4247-0.1346-0.27790.00020.8482-0.1061-0.36760.8885-0.01491.110543.785534.2234109.1812
263.358-0.12721.43272.0310.64824.9161-0.0568-0.1761-0.141-0.11470.0702-0.4228-0.54120.4565-00.81210.06060.09321.2224-0.06321.186876.059949.166816.8554
275.8072-0.66080.82963.07172.51963.81270.07820.45440.2126-0.1814-0.2163-0.63940.14950.36110.00020.95550.02830.47221.0080.11551.07566.177857.4282-31.9557
284.15310.2092-2.12632.4770.26275.6464-0.2782-0.15330.29530.05540.00330.54280.2007-0.0835-0.00010.8715-0.0352-0.11431.03060.15521.197633.997342.7677157.8216
293.4277-1.7498-1.51683.2047-0.19412.0359-0.14310.73120.77750.0623-0.271-1.2884-0.16350.0876-0.00031.6050.2474-0.14882.16480.23311.506684.731624.226881.4638
303.5479-0.8342-2.92415.65262.12075.23080.0929-0.3480.51250.31690.4359-0.1882-0.72870.41460.00081.76070.1808-0.19381.9426-0.22281.192658.854566.212660.8317
312.6581-2.17330.94083.4606-0.63394.87570.17640.7741-0.5148-0.2119-0.57850.97040.444-0.3627-0.00061.47740.2950.11711.8864-0.17251.246824.974367.4928-59.3016
324.449-1.1405-1.5311.52160.77864.3722-1.0179-0.3363-0.2539-0.01070.8025-0.23831.07480.42090.00042.9133-0.02550.11892.12930.17641.582849.918425.7162201.842
332.4722-0.994-0.46035.8795-1.47854.86690.24770.506-0.3208-0.3507-0.1235-0.27470.4139-0.53820.00041.1971-0.3238-0.32331.2906-0.1851.318338.102614.2055101.8551
345.7370.3811.24092.48050.79493.2814-0.0592-0.58890.01670.26370.056-0.27840.3980.55310.00031.02290.1499-0.03911.17710.17791.165468.242930.282724.7946
353.0466-0.5640.02574.77262.03014.87770.20030.53020.115-0.276-0.08430.1299-0.2060.5262-0.00021.2957-0.12540.54641.38870.24621.379871.593477.3212-39.2435
366.18240.1793-1.18573.448-1.38894.4027-0.0769-0.55730.21160.48130.0605-0.0181-0.6612-0.35030.00061.25110.0558-0.04241.0972-0.261.341241.802561.6409165.7767
374.31170.86770.03071.294-0.73651.4589-0.16171.6668-0.0691-0.7448-0.1692-0.30490.09120.1988-01.61560.1599-0.07511.89610.07721.6108134.292711.125291.9492
387.58240.8403-1.48192.07420.21313.2734-0.21521.3771-0.0654-0.37420.06590.16670.228-0.17540.00010.88890.107-0.01851.0792-0.04210.7899-24.413581.7021-48.469
393.6570.15030.11233.0256-0.74624.52620.2533-1.13140.42931.379-0.4014-0.128-2.3627-0.9643-03.17270.53490.17882.3075-0.14141.60617.699594.830375.8399
402.4154-0.4097-1.12064.16090.74192.94-0.0810.68570.8152-0.5707-0.29931.4451-0.3134-0.1277-0.00021.90270.0085-0.71741.74820.02841.776631.07251.113577.1802
412.25010.29230.24813.42570.63223.2621-0.03390.60280.1085-0.244-0.2496-1.1105-0.0270.68410.00012.13320.15580.50872.02260.14721.597679.352140.7795-63.6735
427.75631.02921.77284.6067-1.35613.66850.1474-1.3347-0.31640.30590.2576-0.23640.22750.56580.00021.47170.1340.03232.02820.0221.9326108.263740.308732.5085
435.93580.50510.21073.07511.2461-0.6285-0.1604-0.72950.12060.63380.2219-0.2702-0.3528-0.52980.00011.44380.13110.17162.0091-0.07991.88071.773451.9385172.7879
444.48521.0639-2.2474.4844-1.18648.37960.03790.5480.3474-1.00650.1265-0.25771.0104-0.047301.38860.08260.19940.9379-0.0880.640256.728123.8242-42.1504
455.87120.1518-0.12585.7621.42643.25120.018-0.95560.31870.8536-0.45560.47880.1113-0.5404-01.446-0.38680.14081.72770.04821.39259.808516.3612163.9418
464.7295-0.3492-0.02294.3148-0.42684.93830.0053-0.8136-0.32160.8237-0.1649-0.4132-0.14460.7678-0.00011.4221-0.42830.00011.8036-0.03641.584799.987275.556622.97
476.75150.30710.83733.88781.12977.03550.27490.8073-0.0618-0.82740.00850.2018-0.97480.3490.00011.3432-0.0743-0.16140.90930.20540.864453.613567.753598.9073
484.39480.9299-1.36856.18-1.353.9072-0.1659-0.2697-0.28250.178-0.08030.02350.80110.139601.2291-0.08120.26880.8190.00081.021641.45676.3862-7.5643
493.3460.31840.83114.24211.26374.23280.33540.3349-0.90560.2968-0.1573-0.54130.55790.3796-01.3072-0.1955-0.17731.33680.03772.000320.9931-13.809137.4953
501.90080.3442-0.71922.6881-0.43962.76340.33270.2411.02730.1704-0.19310.4781-0.7913-0.4271-01.5402-0.1640.45461.68290.10922.417888.9973105.809-3.4462
513.30640.97991.02875.43430.97163.3274-0.1327-0.29760.20540.5428-0.1088-0.3292-0.4521-0.203501.2863-0.1114-0.31090.89510.09371.250768.874485.0904133.4295
524.72360.69111.86995.65420.0716.28820.01370.0875-0.15870.709-0.0769-0.55720.15850.4177-0.00040.92510.17410.32070.8302-0.08090.730767.634337.0996-11.936
535.4348-0.1546-1.75523.36230.13355.60330.1045-0.0752-0.16650.9213-0.28370.29680.1168-0.296-0.00021.1685-0.0182-0.31830.72330.22121.149142.553654.5814129.0454
542.04180.5286-0.80581.36660.32735.23620.3380.01280.8092-0.22140.0164-0.7033-0.3024-0.1592-00.8429-0.08230.20831.1436-0.01051.35282.613465.8206-5.3156
553.0746-0.37060.78482.4599-0.28373.71450.11880.2189-0.4873-0.24130.39450.4285-0.21570.281300.7849-0.2025-0.03870.9622-0.0451.391727.413226.0213135.7657
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 1:104
2X-RAY DIFFRACTION2CHAIN E AND RESID 1:104
3X-RAY DIFFRACTION3CHAIN C AND RESID 1:104
4X-RAY DIFFRACTION4CHAIN G AND RESID 1:104
5X-RAY DIFFRACTION5CHAIN A AND RESID 105:209
6X-RAY DIFFRACTION6CHAIN E AND RESID 105:209
7X-RAY DIFFRACTION7CHAIN C AND RESID 105:209
8X-RAY DIFFRACTION8CHAIN G AND RESID 105:209
9X-RAY DIFFRACTION9CHAIN A AND RESID 210:328
10X-RAY DIFFRACTION10CHAIN E AND RESID 210:328
11X-RAY DIFFRACTION11CHAIN C AND RESID 210:328
12X-RAY DIFFRACTION12CHAIN G AND RESID 210:328
13X-RAY DIFFRACTION13CHAIN A AND RESID 329:426
14X-RAY DIFFRACTION14CHAIN E AND RESID 329:426
15X-RAY DIFFRACTION15CHAIN C AND RESID 329:426
16X-RAY DIFFRACTION16CHAIN G AND RESID 329:426
17X-RAY DIFFRACTION17CHAIN A AND RESID 427:534
18X-RAY DIFFRACTION18CHAIN E AND RESID 427:534
19X-RAY DIFFRACTION19CHAIN C AND RESID 427:534
20X-RAY DIFFRACTION20CHAIN G AND RESID 427:534
21X-RAY DIFFRACTION21(CHAIN A AND RESID 535:578) OR (CHAIN B AND RESID 746:806)
22X-RAY DIFFRACTION22(CHAIN E AND RESID 535:578) OR (CHAIN F AND RESID 746:806)
23X-RAY DIFFRACTION23(CHAIN C AND RESID 535:578) OR (CHAIN D AND RESID 746:806)
24X-RAY DIFFRACTION24(CHAIN G AND RESID 535:578) OR (CHAIN H AND RESID 746:806)
25X-RAY DIFFRACTION25CHAIN B AND (RESID 807:911 OR RESID 727-745)
26X-RAY DIFFRACTION26CHAIN F AND (RESID 807:911 OR RESID 727-745)
27X-RAY DIFFRACTION27CHAIN D AND (RESID 807:911 OR RESID 727-745)
28X-RAY DIFFRACTION28CHAIN H AND (RESID 807:911 OR RESID 727-745)
29X-RAY DIFFRACTION29(CHAIN B AND RESID 912:969) OR (CHAIN B AND RESID 1269:1330)
30X-RAY DIFFRACTION30(CHAIN F AND RESID 912:969) OR (CHAIN F AND RESID 1269:1330)
31X-RAY DIFFRACTION31(CHAIN D AND RESID 912:969) OR (CHAIN D AND RESID 1269:1330)
32X-RAY DIFFRACTION32(CHAIN H AND RESID 912:969) OR (CHAIN H AND RESID 1269:1330)
33X-RAY DIFFRACTION33CHAIN B AND RESID 1331:1495
34X-RAY DIFFRACTION34CHAIN F AND RESID 1331:1495
35X-RAY DIFFRACTION35CHAIN D AND RESID 1331:1495
36X-RAY DIFFRACTION36CHAIN H AND RESID 1331:1495
37X-RAY DIFFRACTION37CHAIN B AND RESID 970:1268
38X-RAY DIFFRACTION38CHAIN D AND RESID 970:1268
39X-RAY DIFFRACTION39CHAIN F AND RESID 970:1268
40X-RAY DIFFRACTION40CHAIN B AND RESID 1496:1641
41X-RAY DIFFRACTION41CHAIN D AND RESID 1496:1641
42X-RAY DIFFRACTION42CHAIN F AND RESID 1496:1641
43X-RAY DIFFRACTION43CHAIN H AND RESID 1496:1641
44X-RAY DIFFRACTION44CHAIN I AND RESID 235:449
45X-RAY DIFFRACTION45CHAIN J AND RESID 235:449
46X-RAY DIFFRACTION46CHAIN K AND RESID 235:449
47X-RAY DIFFRACTION47CHAIN L AND RESID 235:449
48X-RAY DIFFRACTION48CHAIN I AND RESID 450:739
49X-RAY DIFFRACTION49CHAIN J AND RESID 450:739
50X-RAY DIFFRACTION50CHAIN K AND RESID 450:739
51X-RAY DIFFRACTION51CHAIN L AND RESID 450:739
52X-RAY DIFFRACTION52CHAIN M AND RESID 2:82
53X-RAY DIFFRACTION53CHAIN N AND RESID 2:82
54X-RAY DIFFRACTION54CHAIN P AND RESID 2:82
55X-RAY DIFFRACTION55CHAIN Q AND RESID 2:82

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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

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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