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- PDB-5o32: The structure of complement complex -

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基本情報

登録情報
データベース: PDB / ID: 5o32
タイトルThe structure of complement complex
要素
  • (Complement C3) x 2
  • (Complement factor ...) x 3
キーワードIMMUNE SYSTEM / complement / complex / regulation / RCA
機能・相同性
機能・相同性情報


complement factor I / regulation of complement activation, alternative pathway / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / symbiont cell surface / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / regulation of complement-dependent cytotoxicity / complement component C3b binding / vertebrate eye-specific patterning ...complement factor I / regulation of complement activation, alternative pathway / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / symbiont cell surface / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / regulation of complement-dependent cytotoxicity / complement component C3b binding / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / regulation of complement activation / 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 / heparan sulfate proteoglycan binding / positive regulation of D-glucose transmembrane transport / serine-type endopeptidase complex / 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 / heparin binding / 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 / innate immune response / serine-type endopeptidase activity / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
: / : / Complement factor I, FIMAC N-terminal domain / Complement factor I, KAZAL domain / Factor I / membrane attack complex / factor I membrane attack complex / : / Scavenger receptor cysteine-rich domain / Complement C3-like, NTR domain / : ...: / : / Complement factor I, FIMAC N-terminal domain / Complement factor I, KAZAL domain / Factor I / membrane attack complex / factor I membrane attack complex / : / Scavenger receptor cysteine-rich domain / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / 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 / Kazal domain superfamily / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Kazal domain / Kazal domain profile. / Macroglobulin domain MG4 / Macroglobulin domain MG4 / 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 / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / 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 / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulin-like fold / Peptidase S1, PA clan
類似検索 - ドメイン・相同性
MALONATE ION / Complement C3 / Complement factor I / Complement factor H
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: 4.20620907647 Å
データ登録者Xue, X. / Wu, J. / Forneris, F. / Gros, P.
資金援助 オランダ, 米国, 3件
組織認可番号国
ERC Advanced grant233229 オランダ
NWO Spinoza01.80.104.00 オランダ
NIH R01AI030040-16 米国
引用ジャーナル: Nat. Struct. Mol. Biol. / 年: 2017
タイトル: Regulator-dependent mechanisms of C3b processing by factor I allow differentiation of immune responses.
著者: Xue, X. / Wu, J. / Ricklin, D. / Forneris, F. / Di Crescenzio, P. / Schmidt, C.Q. / Granneman, J. / Sharp, T.H. / Lambris, J.D. / Gros, P.
履歴
登録2017年5月23日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年6月28日Provider: repository / タイプ: Initial release
改定 1.12017年7月12日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
改定 1.22017年8月16日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32019年10月16日Group: Data collection / カテゴリ: reflns_shell
改定 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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_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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _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.pdbx_value_order / _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
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12024年11月6日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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: Complement C3
B: Complement C3
C: Complement factor H,Complement factor H
D: Complement factor I
I: Complement factor I
E: Complement C3
F: Complement C3
G: Complement factor H,Complement factor H
H: Complement factor I
J: Complement factor I
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)569,30633
ポリマ－563,63810
非ポリマー5,66723
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area55510 Å2
ΔGint-107 kcal/mol
Surface area221440 Å2
手法PISA
単位格子
Length a, b, c (Å)116.370, 122.790, 157.200
Angle α, β, γ (deg.)69.764, 76.101, 70.130
Int Tables number1
Space group name H-MP1
Space group name HallP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
13
23

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain B and (resseq 752:778 or resseq 780:878 or resseq...B752 - 778
121(chain B and (resseq 752:778 or resseq 780:878 or resseq...B780 - 878
131(chain B and (resseq 752:778 or resseq 780:878 or resseq...B880 - 936
141(chain B and (resseq 752:778 or resseq 780:878 or resseq...B938 - 952
151(chain B and (resseq 752:778 or resseq 780:878 or resseq...B955 - 987
161(chain B and (resseq 752:778 or resseq 780:878 or resseq...B991 - 1305
171(chain B and (resseq 752:778 or resseq 780:878 or resseq...B1307 - 1351
181(chain B and (resseq 752:778 or resseq 780:878 or resseq...B1354 - 1371
191(chain B and (resseq 752:778 or resseq 780:878 or resseq...B1381 - 1495
1101(chain B and (resseq 752:778 or resseq 780:878 or resseq...B1499
1111(chain B and (resseq 752:778 or resseq 780:878 or resseq...B1502 - 1575
1121(chain B and (resseq 752:778 or resseq 780:878 or resseq...B1577 - 1578
1131(chain B and (resseq 752:778 or resseq 780:878 or resseq...B1581 - 1591
1141(chain B and (resseq 752:778 or resseq 780:878 or resseq...B1593 - 1614
1151(chain B and (resseq 752:778 or resseq 780:878 or resseq...B1616 - 1662
211(chain F and (resseq 752:778 or resseq 780:878 or resseq...F752 - 778
221(chain F and (resseq 752:778 or resseq 780:878 or resseq...F780 - 878
231(chain F and (resseq 752:778 or resseq 780:878 or resseq...F880 - 936
241(chain F and (resseq 752:778 or resseq 780:878 or resseq...F938 - 952
251(chain F and (resseq 752:778 or resseq 780:878 or resseq...F955 - 987
261(chain F and (resseq 752:778 or resseq 780:878 or resseq...F991 - 1305
271(chain F and (resseq 752:778 or resseq 780:878 or resseq...F1307 - 1351
281(chain F and (resseq 752:778 or resseq 780:878 or resseq...F1354 - 1371
291(chain F and (resseq 752:778 or resseq 780:878 or resseq...F1381 - 1495
2101(chain F and (resseq 752:778 or resseq 780:878 or resseq...F1499
2111(chain F and (resseq 752:778 or resseq 780:878 or resseq...F1502 - 1575
2121(chain F and (resseq 752:778 or resseq 780:878 or resseq...F1577 - 1578
2131(chain F and (resseq 752:778 or resseq 780:878 or resseq...F1581 - 1591
2141(chain F and (resseq 752:778 or resseq 780:878 or resseq...F1593 - 1614
2151(chain F and (resseq 752:778 or resseq 780:878 or resseq...F1616 - 1662
122(chain H and (resseq 27:166 or resseq 169 or resseq...H27 - 166
132(chain H and (resseq 27:166 or resseq 169 or resseq...H169
142(chain H and (resseq 27:166 or resseq 169 or resseq...H171 - 172
152(chain H and (resseq 27:166 or resseq 169 or resseq...H178 - 182
162(chain H and (resseq 27:166 or resseq 169 or resseq...H184 - 186
172(chain H and (resseq 27:166 or resseq 169 or resseq...H188 - 200
182(chain H and (resseq 27:166 or resseq 169 or resseq...H204
192(chain H and (resseq 27:166 or resseq 169 or resseq...H208
1102(chain H and (resseq 27:166 or resseq 169 or resseq...H210 - 217
1112(chain H and (resseq 27:166 or resseq 169 or resseq...H228 - 236
1122(chain H and (resseq 27:166 or resseq 169 or resseq...H238 - 294
1132(chain H and (resseq 27:166 or resseq 169 or resseq...H306 - 322
1142(chain H and (resseq 27:166 or resseq 169 or resseq...H325 - 330
1152(chain H and (resseq 27:166 or resseq 169 or resseq...H340 - 395
1162(chain H and (resseq 27:166 or resseq 169 or resseq...H397 - 404
1172(chain H and (resseq 27:166 or resseq 169 or resseq...H406 - 418
1182(chain H and (resseq 27:166 or resseq 169 or resseq...H420 - 441
1192(chain H and (resseq 27:166 or resseq 169 or resseq...H443 - 470
1202(chain H and (resseq 27:166 or resseq 169 or resseq...H473 - 475
1212(chain H and (resseq 27:166 or resseq 169 or resseq...H477 - 550
1222(chain H and (resseq 27:166 or resseq 169 or resseq...H553
1232(chain H and (resseq 27:166 or resseq 169 or resseq...H555 - 567
1242(chain H and (resseq 27:166 or resseq 169 or resseq...H569 - 575
1252(chain H and (resseq 27:166 or resseq 169 or resseq...H577 - 580
1262(chain H and (resseq 27:166 or resseq 169 or resseq...H670
1272(chain H and (resseq 27:166 or resseq 169 or resseq...H703
212(chain D and (resseq 27:166 or resseq 169 or resseq...D27 - 166
222(chain D and (resseq 27:166 or resseq 169 or resseq...D169
232(chain D and (resseq 27:166 or resseq 169 or resseq...D171 - 172
242(chain D and (resseq 27:166 or resseq 169 or resseq...D178 - 182
252(chain D and (resseq 27:166 or resseq 169 or resseq...D184 - 186
262(chain D and (resseq 27:166 or resseq 169 or resseq...D188 - 200
272(chain D and (resseq 27:166 or resseq 169 or resseq...D204
282(chain D and (resseq 27:166 or resseq 169 or resseq...D208
292(chain D and (resseq 27:166 or resseq 169 or resseq...D210 - 217
2102(chain D and (resseq 27:166 or resseq 169 or resseq...D228 - 236
2112(chain D and (resseq 27:166 or resseq 169 or resseq...D238 - 294
2122(chain D and (resseq 27:166 or resseq 169 or resseq...D306 - 322
2132(chain D and (resseq 27:166 or resseq 169 or resseq...D325 - 330
2142(chain D and (resseq 27:166 or resseq 169 or resseq...D340 - 395
2152(chain D and (resseq 27:166 or resseq 169 or resseq...D397 - 404
2162(chain D and (resseq 27:166 or resseq 169 or resseq...D406 - 418
2172(chain D and (resseq 27:166 or resseq 169 or resseq...D420 - 441
2182(chain D and (resseq 27:166 or resseq 169 or resseq...D443 - 470
2192(chain D and (resseq 27:166 or resseq 169 or resseq...D473 - 475
2202(chain D and (resseq 27:166 or resseq 169 or resseq...D477 - 550
2212(chain D and (resseq 27:166 or resseq 169 or resseq...D553
2222(chain D and (resseq 27:166 or resseq 169 or resseq...D555 - 567
2232(chain D and (resseq 27:166 or resseq 169 or resseq...D569 - 575
2242(chain D and (resseq 27:166 or resseq 169 or resseq...D577 - 580
2252(chain D and (resseq 27:166 or resseq 169 or resseq...D670
2262(chain D and (resseq 27:166 or resseq 169 or resseq...D703
113(chain A and (resseq 23:97 or resseq 101:445 or (resid...A23 - 97
123(chain A and (resseq 23:97 or resseq 101:445 or (resid...A101 - 480
133(chain A and (resseq 23:97 or resseq 101:445 or (resid...A482 - 664
143(chain A and (resseq 23:97 or resseq 101:445 or (resid...A1669 - 1672
153(chain A and (resseq 23:97 or resseq 101:445 or (resid...A1674
213(chain E and (resseq 23:97 or resseq 101:445 or (resid...E23 - 97
223(chain E and (resseq 23:97 or resseq 101:445 or (resid...E101 - 480
233(chain E and (resseq 23:97 or resseq 101:445 or (resid...E482 - 664
243(chain E and (resseq 23:97 or resseq 101:445 or (resid...E1669 - 1672
253(chain E and (resseq 23:97 or resseq 101:445 or (resid...E1674

NCSアンサンブル:
ID
1
2
3

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要素

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タンパク質 , 2種, 4分子 AEBF

#1: タンパク質 Complement C3 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1


分子量: 71393.320 Da / 分子数: 2 / 断片: beta chain, UNP 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 C3 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1


分子量: 104073.164 Da / 分子数: 2 / 断片: alpha chain, UNP residues 749-1663 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P01024

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Complement factor ... , 3種, 6分子 CGDHIJ

#3: タンパク質 Complement factor H,Complement factor H / H factor 1


分子量: 42767.074 Da / 分子数: 2
断片: UNP residues 19-264,UNP residues 1107-1230,UNP residues 19-264,UNP residues 1107-1230
由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CFH, HF, HF1, HF2 / 細胞株 (発現宿主): HEK293E / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P08603
#4: タンパク質 Complement factor I / C3B/C4B inactivator


分子量: 35963.117 Da / 分子数: 2 / 断片: UNP Residues 19-339 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CFI, IF / 細胞株 (発現宿主): HEK293E / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P05156, complement factor I
#5: タンパク質 Complement factor I / C3B/C4B inactivator


分子量: 27622.352 Da / 分子数: 2 / 断片: UNP Residues 340-583 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CFI, IF / 細胞株 (発現宿主): HEK293E / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P05156, complement factor I

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糖 , 3種, 16分子

#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
DManpb1-3[DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#7: 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: 2 / 由来タイプ: 合成
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)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#9: 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: 12 / 由来タイプ: 合成 / 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, 7分子

#8: 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: 6 / 由来タイプ: 組換発現 / 式: Ca
#10: 化合物 ChemComp-MLI / MALONATE ION / マロナ-ト


分子量: 102.046 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C3H2O4

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詳細

Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.56 Å3/Da / 溶媒含有率: 65.47 %
結晶化温度: 291.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 60mM sodium malonate PH5.0 6% w/v PEG3350

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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: ID23-1 / 波長: 0.988 Å
検出器タイプ: DECTRIS PILATUS 2M / 検出器: PIXEL / 日付: 2015年5月4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: 0.988 Å / 相対比: 1
反射解像度: 4.2→49.2 Å / Num. obs: 55430 / % possible obs: 93.4 % / 冗長度: 3.5 % / Biso Wilson estimate: 83.4330841818 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.109 / Net I/σ(I): 6.1

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
XDS20161101データ削減
Aimless0.5.32データスケーリング
PHASER2.7.17位相決定
精密化構造決定の手法: 分子置換 / 解像度: 4.20620907647→49.1341944258 Å / SU ML: 0.513056330322 / 交差検証法: FREE R-VALUE / σ(F): 1.98620697036 / 位相誤差: 25.322159147
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.254066763601 2622 5.08238030626 %
Rwork0.228893404061 48968 -
obs0.230193326461 51590 93.4059965238 %
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: 108.243236439 Å2
精密化ステップサイクル: LAST / 解像度: 4.20620907647→49.1341944258 Å
タンパク質核酸リガンド溶媒全体
原子数38732 0 359 0 39091
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0036513812417240042
X-RAY DIFFRACTIONf_angle_d0.83811035866154225
X-RAY DIFFRACTIONf_chiral_restr0.04968024295816020
X-RAY DIFFRACTIONf_plane_restr0.004508057864496976
X-RAY DIFFRACTIONf_dihedral_angle_d14.515568017524380
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2062-4.28270.309383653745260.306571806785485X-RAY DIFFRACTION17.3750425026
4.2827-4.3650.3124740455411150.3037935418271675X-RAY DIFFRACTION62.6531326566
4.365-4.4540.2702519417251470.2966030169362711X-RAY DIFFRACTION97.4761255116
4.454-4.55080.3056119035171510.2673622529482751X-RAY DIFFRACTION99.9311294766
4.5508-4.65660.2824564237781600.2544787767612752X-RAY DIFFRACTION99.897084048
4.6566-4.77290.2707608424471680.2493436201982742X-RAY DIFFRACTION99.8627316404
4.7729-4.90190.2810200397141470.2467551871312771X-RAY DIFFRACTION99.9315068493
4.9019-5.0460.2820620594661290.2488050730592765X-RAY DIFFRACTION100
5.046-5.20870.2770540527591360.2408537069582738X-RAY DIFFRACTION99.9304589708
5.2087-5.39460.2771983683051350.2480305652482763X-RAY DIFFRACTION99.9655053467
5.3946-5.61030.3188066170941180.2431967533832825X-RAY DIFFRACTION99.9660326087
5.6103-5.86530.2683792214241570.2581922395982735X-RAY DIFFRACTION99.861878453
5.8653-6.17390.296169680251430.2564489256822753X-RAY DIFFRACTION99.8276456394
6.1739-6.55990.2659720261211500.2460972694162771X-RAY DIFFRACTION99.8974008208
6.5599-7.0650.2606770753551500.2382742702132733X-RAY DIFFRACTION99.9306759099
7.065-7.77350.2710356007351430.2182617849622781X-RAY DIFFRACTION99.9658119658
7.7735-8.89260.2188024714271530.1879709480542746X-RAY DIFFRACTION99.9655172414
8.8926-11.18190.1557756050861320.1498611689332744X-RAY DIFFRACTION99.4467496542
11.1819-49.13750.1817344332951620.1651678872162727X-RAY DIFFRACTION99.312478515
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)
11.86562547881.06861735970.3096863819535.44459078484-0.666095552194.39913733516-0.817009103151-0.2288944701340.12131628964-0.9483191892961.004196660030.9566877240610.295307237565-0.5939759833040.740477566050.5680527850070.278709643797-0.01426785690060.6276516825470.06739368522710.6935904481572.15919549528-37.4218984746-52.6488873124
24.359711994091.52798934726-2.044532182272.701507194840.3347697052591.592066445350.541158827599-0.630464838808-0.5770276156460.102434544263-0.452564987104-0.6904395009270.2566337638580.836543029381-0.01902202072030.3568487033470.5161680635830.1537602617730.733056669782-0.04555683820230.26882157271211.0860212544-38.8867345635-17.7009343018
32.493091369890.8554729633870.1323623017113.9603621235-2.300218768012.38105547930.519898375333-0.9493545592360.4077029556810.0851209554769-0.955791708521-0.370279108954-0.6008862093550.9055410325150.5237554148181.43557971004-0.4519518607110.01034247113241.487461231950.1394678285970.66867892125231.2927894184-10.0149919241-7.87059324921
45.365425346633.614369789871.59465618525.245668432752.858812228468.90825792501-0.288845671391-0.2132957114880.3598690925820.2385951274120.3383952848320.599198954111-0.1528761528880.843744253915-0.02272515522590.8156555398520.108672974119-0.01503372676180.4945177658480.02715814716950.62649569273823.884499052-5.42743679913-41.7031256337
55.005097727670.2771706488670.8127204870373.6874805842-0.563321635934.338854646840.04402008819960.5582429875890.881810283998-0.7660415163930.3899911322020.562890285337-0.833315346536-0.055441093898-0.3944261567991.094725052760.1932973290020.0732009598260.5322355444970.103274770690.6197455046025.60518612612-15.4227327971-53.5928543945
60.978226447704-0.193522544348-0.5994127465570.987367713657-0.1449941240071.394105892350.379808579411-0.5281900648780.2744587168780.478254484228-0.2571073183280.596127250414-0.6693591733250.1188581133550.481947225490.8216637806310.2490554588190.590222638770.893854000384-0.3048749547950.581846910511-3.13650987806-21.8527187953-6.36374493437
71.286995494610.5631040888380.2737705721240.732718761414-0.2303227423990.271098771498-0.225579766432-0.26847588769-0.3540800344510.01406081925710.580251696894-0.2252755879210.5295072157780.539784762006-0.07952557264640.3059528020040.3716171279370.001762895315450.8543078417080.06924121760780.67168838136314.7680391938-26.7702227263-40.2064790772
80.5938587673590.471761623587-0.4473885322320.505578978772-0.9400775132982.992722431290.264405385352-0.5417803213380.1984972990391.16772542912-0.4569060737370.288336146017-0.581606643940.067911654236-0.007033882680671.45086238132-0.4299143372140.153443944411.43580811981-0.1990935937240.54211716738611.5302545533-22.8966368818.78814064
91.63690975788-1.688794533350.2273974528572.54768992143-1.661578440335.285456892310.353787658141-0.04160712877390.6841489549081.05764971545-0.62757433901-0.634798443954-0.7315436267080.9012754194980.3596593421431.65619859086-0.653203632289-0.2303184993782.031133047920.1839707179350.78108015556732.6420178694-15.516700195420.3164648634
100.4071547982310.6068947837580.8544064142090.9482863130630.7175020885253.911436481810.327658394968-0.477092036826-0.3508957143240.15780557387-0.0701562103275-0.3214885581460.887282946230.488136543077-0.2832486769340.9403865021460.352424553155-0.107278275731.692575680650.0380532450291.1710959270825.2404170985-59.1404587748-7.33544776103
113.87782593514-0.0831617489889-0.1179831445273.911848436241.793554317510.845028699749-0.41225776779-0.335036555526-0.3022959024491.619179482440.439767014820.217996401083-0.9284454632180.380264945766-0.3398151331282.2961164556-0.424899689641-0.05886255033011.632492729310.4494179769160.85473803395826.6919351763-38.285368755928.2668358675
124.142955725530.556974986639-0.9868301229952.66697332901-0.09215608117070.3098786749050.165387184969-0.4979887635990.04864642123380.210993981612-0.2512890417240.0718748867914-0.2934706425320.8869075795480.1279990470461.3304418144-0.360994135869-0.2112741283591.841774029030.2033325194960.76352577269813.653393548-47.994133660246.4485552184
133.38558538666-0.8135758465170.5654389651262.55134621368-0.6603588883612.355365972490.105277513136-0.331976952866-0.8252982922680.1421975743820.66220949627-0.4509877792750.377717989597-0.0471839945244-0.2316316690610.349572169820.2979025982420.09787335376160.702780185765-0.396391244780.6273123508124.9536913045-68.1715988664-61.8420893065
141.930728602171.07499264527-0.3751336118571.13971490547-0.8952887362640.945661074752-0.386665054123-0.2453953963760.5095412811660.6922338211340.09019584635790.714974877786-0.0397409607359-0.5184297189020.1933862028571.673765354170.02150214487760.4993675795341.26716632235-0.3602895005081.02270104363-20.9971557626-16.402930666432.4710606382
152.38141082011-1.66005413766-0.3389682964337.831105112911.633160058622.159531063850.3808970511790.1818304259230.6987993805370.339940888533-0.903000039575-0.116570533590.284090298949-1.295642030580.4788446459010.6560198218130.05152851831450.2133416902790.899156705533-0.1311418489880.540824118844-9.00989197983-36.52862107983.85050007035
164.96136569587-0.437194672041-3.216529765164.122055618990.1374587789265.01328767956-0.9824720114830.612702656899-0.5817323797270.2084600075220.4044170507070.09744302240421.882485822080.1759818747770.4120041187331.237590743270.08829068827670.2293613036580.602373189030.05916739896250.601882885125-0.312337044004-59.0682691767-24.7380570247
173.73896531953.21955387515-5.165893464035.54043643104-5.057579804947.959112364350.38791122410.8103812066580.6477516570950.3598907978671.319461929042.33204439163-1.17325702519-1.88437140656-1.655198423950.837757723750.2229273959020.04115363481351.2806690090.1240385536841.1756524775-0.995483616584-61.6623590388-58.8401544828
187.125605829122.858113341111.344740362656.325560874531.940832835627.51044501439-0.711065654154-0.248814762824-0.445567490666-0.726350479982-0.09869812624640.4412469774941.64338615169-2.56445612960.6369614594561.39601892107-0.361937285756-0.1783536596591.229320203560.1422467589721.1865892209-0.801426002319-86.069248425-73.0975169748
190.22120338926-0.2957106750970.3504646835642.68841200165-0.7060547397663.189768296470.960820749756-0.558821045241-1.647002735680.424760259251-0.2346116600270.08789259502880.338082442921.42625555907-0.6652463053981.216233115180.101169618979-0.1521366276891.70635502884-0.1181151430641.9972366693927.1832160269-105.852595685-77.120104004
201.566452390290.04157891143410.01851765332163.655994242110.09327559066981.567817178090.09606996560480.128937857392-0.0582740626074-0.246199847908-0.0445498469789-0.07305843122550.3032484698610.0701667474168-0.03930016973871.27325494395-0.162107197277-0.2494769419391.270190625120.3949294883610.739315531556-6.7211586359-81.482016361448.3704331182
212.682316775330.1250797577110.3146106385893.29289773322-1.399463423774.079293542080.49947442711-0.18583406754-0.4081731726770.447755020018-0.733855145205-0.469295387971.036964458550.5542670656760.1999536760521.263701895520.0435659679949-0.06065923701750.9729276684040.2494798400760.5931040501951.97146318115-66.638383774610.4005402754
225.835572482670.006434531959-1.844072021296.141023661030.09730181343674.8538578654-0.898268992446-0.3857391621950.413720995988-0.5119684727030.208573986005-1.230190033950.440905962910.2557845829280.5134387154451.02195283784-0.014415695004-0.1890008896730.3690524256560.04523926206790.685181344488-30.3536586286-83.9259516246-54.2604274671
233.268079214990.02132070316581.342517466392.21115038439-0.3203635371432.445571015940.298178361341-0.1598877682540.0209339281716-0.2564871765740.209785724760.2865603074360.160179415862-1.11770758182-0.3426174249340.4973242790540.273589474878-0.1654502108710.6143620510650.0572737577780.378364731722-46.3963163052-79.9694490761-21.9804949344
244.051160749682.748141241053.182833356215.270062753773.409914370473.13730067911-0.0620609090566-0.4685557310010.1537179701910.0303995727595-0.7591319796690.9719060766840.337087946996-0.8109875023020.8228633308210.87407114456-0.1494259337230.1960583183431.216758739-0.1936744450510.828015840084-67.9359113863-108.407332875-14.2802199152
255.02583911822.32491376145-2.49902295237.11177454954-1.789518118452.60235437892-0.61075654702-0.1361888774350.0279901854403-0.9852882008090.3255523248460.03273265892450.0992671650734-0.375327703950.2261356000360.692686392878-0.0720466853436-0.2586782461160.576199921517-0.0640457216480.965951923834-53.9760366731-115.30900697-45.6634257406
262.24339027986-0.142195364641-0.1251970047612.694101204392.556942168752.70242638361-0.271143147190.367741466112-0.449089665817-0.9984887619930.475157056616-0.3608139390040.932136541956-0.0697610766308-0.09979746470321.68207793525-0.0263053930690.05535196724290.441772684706-0.1385881522550.731639976912-33.6049936496-106.008369038-54.2295986504
271.25970900634-0.5246294643440.5435011006741.08776908164-0.77579636843.334598651890.387476123385-0.358474258228-0.2809058448730.755486358579-0.311579714569-0.615601616550.02923644653520.110580008573-0.02839442784270.743339615673-0.057195339576-0.3191156111690.78308987610.1667303328890.569390937484-34.5551810868-95.8332504594-6.78413397274
281.3713461980.1954458266150.1483655168943.722550126360.5116745848460.0825122378432-0.0749000742073-0.4320280702320.407378112988-1.171929256260.5597451774240.091498542711-0.0775918353101-0.6808419124631.760947562630.1960652398430.188147424461-0.3266890615290.918415833297-0.05961135593070.479950053795-45.3263274613-93.7503214325-43.8736153247
291.39234892670.155376531839-0.3713428227495.911121555750.9315277711362.192951398530.107746979877-0.428151628244-0.03115535111431.35526961015-0.4366043319770.2450600701790.58441232311-0.3419338165690.3593021000020.965285010922-0.1682435777080.05816910550411.263176570340.003713942103770.566980196968-53.974248949-93.113894269614.8057142531
302.04329311478-0.4551038116010.6373656723473.32737114219-0.4393783916342.58859509439-0.3012072647830.200372903935-0.590956150630.863556653469-0.3727937319960.672065091542-0.0744857004711-0.5752752817860.5754674161941.14278662032-0.3382406540430.497585754631.78283418362-0.2179866487851.06485238989-74.8532462556-101.01602984912.6300182678
312.348956939851.08243770102-1.040328620481.89310706638-1.205770062474.92463954290.307083973002-0.2268902053280.2090563096130.06350221841350.04722333724950.572907851047-0.714331366371-0.692952383151-0.390562433360.8263434727470.39473044442-0.07118748414771.338864574460.021405455370.904325321028-62.3971965743-59.3404876528-15.9029777332
321.655038976271.218127542190.3069764728375.99582114768-2.949595222182.02967486537-1.08009907232-0.6752755135050.689680201325-0.03104542997860.989478489602-0.0904606280331.57462575614-0.52233458580.2099127351251.811373162210.1366767727690.3960015192761.66031744645-0.6832368295571.27810338498-70.3184443659-77.326647189120.1867290225
335.471878220271.230022644714.225317699176.609465406060.5788009189714.14426972782-0.279147175375-0.639517098668-0.5755008421080.320885145292-0.0359460543747-0.2612485228260.567707293002-0.5454484757490.2670811398170.768347495790.002611690292930.2804521007621.35140910627-0.1368042422060.995231568117-61.4995258016-65.93789761339.6694369017
343.74280029992-0.9666989892240.1331400260412.85787561867-0.3540606613122.50760127583-0.0534385625050.4254496661811.23561852305-0.0389043689010.2268395028720.201897412973-0.184210559993-0.294167246885-0.01550750270240.311339013380.152217141245-0.1565025899840.7573050440890.2327509902770.91537569824-52.4435322896-54.1899539108-69.4672397714
351.4304022684-0.1485764808490.1241573664190.43856585150.1331417140370.0565486991197-0.281403757237-0.629187937757-0.6324725005160.9165908126620.757183935622-0.432358166622-1.041990946260.508108529805-0.2306988068542.19245670118-0.28471368598-0.2371975341111.522224764540.481036210910.961774198399-25.071774609-97.818255942835.1825753556
361.91919137413-1.81109784755-0.9442484092034.24958531632-0.02842322167551.659940288560.689469418382-0.12606769043-0.5358101592570.313991017791-0.5631888766580.0671379184793-0.2287993780391.03464905336-0.08693249413990.7857751509320.047011751455-0.2804003300260.8362519313640.1018045802330.526036171137-30.9468853628-80.31024965873.389840502
372.72623712823-0.6930516498371.193037152533.0036516023-3.842320411244.92246313412-0.8437571843230.03823434224490.333412365103-0.3666426805970.712308307667-0.0950538860919-1.941589044470.5428437571380.1063620718731.60492541624-0.246963567351-0.1454911283010.790709926424-0.07039676641860.474547143038-34.1239702845-60.17192167-28.1555718864
386.960291616463.731592347154.581724389036.444782905411.742675042814.283010789551.461027327291.32200669207-1.597314381810.6746816800110.48009644413-1.038079081361.547613114732.32094357683-1.884853808321.140818270050.138806809998-0.3732757534021.41640770564-0.08271166293461.22931903002-26.7702767459-59.5346389283-61.8784680949
390.6466613063831.20200088773-0.104893435512.24017131343-0.4069365689587.04614935396-0.2942346478520.8158856475211.10137029160.030126700606-0.07127703714380.661288506155-0.9011451779420.7761078055610.412898130150.751285639708-0.108055444657-0.3084974216081.043575804080.4052769910541.41604789206-25.9565074953-35.5134800805-76.5277305593
402.01515238953-1.733204711430.2303327291491.54415972367-0.08787690331840.245075988034-0.102095287437-0.1952821632220.331759741575-0.0205282349322-0.3478819454870.170079885033-0.481288908703-0.9734785777240.4268587878331.00048997820.0846441436813-0.3152231839141.722296943660.6558159404812.73050569881-54.7727423865-18.6071634883-84.7103630721
412.69699412638-0.0277488060352-0.6904973635492.262567514240.2477622910833.15460392434-0.085842008538-0.0779634078424-0.115405443006-0.08871909359170.008143253973780.0514661092978-0.189515050545-0.06393849626120.07043576001850.7734772882590.06478210266530.2050892804630.947046359435-0.2686748459450.586606000576-42.2188388224-31.776463076342.8052117786
423.43786859175-1.13885611936-0.9063005427554.103105005560.7405198573091.436305676740.2142769040920.1712078468710.1406499896150.106838463246-0.2340824195440.425991766989-0.678200236554-0.2256298096520.02380012237251.005968490130.07906136218470.03870588121180.869517569964-0.2018697044770.404123906536-43.2174850074-50.02961802315.25870800781
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 12:126) or (chain A and resseq 1669) or (chain A and resseq 1670) or (chain A and resseq 1671) or (chain A and resseq 1672) or (chain A and resseq 1674)
2X-RAY DIFFRACTION2chain A and resseq 127:228
3X-RAY DIFFRACTION3chain A and resseq 229:349
4X-RAY DIFFRACTION4chain A and resseq 350:447
5X-RAY DIFFRACTION5(chain A and resseq 448:558) or (chain A and resseq 1667)
6X-RAY DIFFRACTION6(chain A and resseq 559:601) or (chain B and resseq 752:827)
7X-RAY DIFFRACTION7chain A and resseq 602:664
8X-RAY DIFFRACTION8chain B and resseq 828:933
9X-RAY DIFFRACTION9(chain B and resseq 1356:1371) or (chain B and resseq 1381:1496)
10X-RAY DIFFRACTION10(chain B and resseq 934:989) or (chain B and resseq 1288:1355) or (chain B and resseq 1939) or (chain B and resseq 1940)
11X-RAY DIFFRACTION11chain B and resseq 1497:1512
12X-RAY DIFFRACTION12chain B and resseq 1518:1663
13X-RAY DIFFRACTION13chain B and resseq 990:1287
14X-RAY DIFFRACTION14chain C and resseq 19:83
15X-RAY DIFFRACTION15chain C and resseq 84:144
16X-RAY DIFFRACTION16chain C and resseq 145:209
17X-RAY DIFFRACTION17chain C and resseq 210:265
18X-RAY DIFFRACTION18chain C and resseq 1107:1166
19X-RAY DIFFRACTION19chain C and resseq 1167:1230
20X-RAY DIFFRACTION20(chain D and resseq 26:295) or (chain D and resseq 302:326) or (chain D and resseq 670) or (chain D and resseq 677) or (chain D and resseq 703) or (chain D and resseq 618) or (chain D and resseq 619)
21X-RAY DIFFRACTION21(chain D and resseq 327:332) or (chain D and resseq 340:580) or (chain D and resseq 636) or (chain D and resseq 664) or (chain D and resseq 694)
22X-RAY DIFFRACTION22(chain E and resseq 12:126) or (chain E and resseq 1669) or (chain E and resseq 1670) or (chain E and resseq 1671) or (chain E and resseq 1672) or (chain E and resseq 1674)
23X-RAY DIFFRACTION23chain E and resseq 127:228
24X-RAY DIFFRACTION24chain E and resseq 229:349
25X-RAY DIFFRACTION25chain E and resseq 350:447
26X-RAY DIFFRACTION26(chain E and resseq 448:558) or (chain E and resseq 1667)
27X-RAY DIFFRACTION27(chain E and resseq 559:601) or (chain F and resseq 752:827)
28X-RAY DIFFRACTION28chain E and resseq 602:664
29X-RAY DIFFRACTION29chain F and resseq 828:933
30X-RAY DIFFRACTION30(chain F and resseq 1356:1371) or (chain F and resseq 1381:1496)
31X-RAY DIFFRACTION31(chain F and resseq 934:989) or (chain F and resseq 1288:1355) or (chain F and resseq 1939) or (chain F and resseq 1940)
32X-RAY DIFFRACTION32chain F and resseq 1497:1512
33X-RAY DIFFRACTION33chain F and resseq 1518:1663
34X-RAY DIFFRACTION34chain F and resseq 990:1287
35X-RAY DIFFRACTION35chain G and resseq 19:83
36X-RAY DIFFRACTION36chain G and resseq 84:144
37X-RAY DIFFRACTION37chain G and resseq 145:209
38X-RAY DIFFRACTION38chain G and resseq 210:265
39X-RAY DIFFRACTION39chain G and resseq 1107:1166
40X-RAY DIFFRACTION40chain G and resseq 1167:1230
41X-RAY DIFFRACTION41(chain H and resseq 26:295) or (chain H and resseq 302:326) or (chain H and resseq 670) or (chain H and resseq 677) or (chain H and resseq 703) or (chain H and resseq 618) or (chain H and resseq 619)
42X-RAY DIFFRACTION42(chain H and resseq 327:332) or (chain H and resseq 340:580) or (chain H and resseq 636) or (chain H and resseq 664) or (chain H and resseq 694) or chain M

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万見について

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お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る