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- PDB-5bk2: Crystal structure of maltose binding protein in complex with a pe... -

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基本情報

登録情報
データベース: PDB / ID: 5bk2
タイトルCrystal structure of maltose binding protein in complex with a peristeric synthetic antibody
要素
  • Maltose-binding periplasmic protein
  • sAB Heavy Chain
  • sAB Light Chain
キーワードSUGAR BINDING PROTEIN / Maltose binding protein / Conformation specific synthetic antibody / Fab fragment
機能・相同性
機能・相同性情報


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
類似検索 - 分子機能
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
alpha-maltose / PHOSPHATE ION / Maltose/maltodextrin-binding periplasmic protein
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.6 Å
データ登録者Mukherjee, S. / Kossiakoff, A.A.
資金援助 米国, 1件
組織認可番号国
Chicago Biomedical Consortium 米国
引用ジャーナル: J. Biol. Chem. / 年: 2018
タイトル: Engineered synthetic antibodies as probes to quantify the energetic contributions of ligand binding to conformational changes in proteins.
著者: Mukherjee, S. / Griffin, D.H. / Horn, J.R. / Rizk, S.S. / Nocula-Lugowska, M. / Malmqvist, M. / Kim, S.S. / Kossiakoff, A.A.
履歴
登録2017年9月12日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年1月17日Provider: repository / タイプ: Initial release
改定 1.12018年1月24日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22018年3月7日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 2.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_conn_type / 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.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12023年9月27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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 2.22024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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
B: Maltose-binding periplasmic protein
A: Maltose-binding periplasmic protein
C: sAB Heavy Chain
H: sAB Heavy Chain
D: sAB Light Chain
L: sAB Light Chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)188,84230
ポリマ－186,5166
非ポリマー2,32624
水3,981221
1
B: Maltose-binding periplasmic protein
C: sAB Heavy Chain
D: sAB Light Chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,54116
ポリマ－93,2583
非ポリマー1,28313
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-77 kcal/mol
Surface area33090 Å2
手法PISA
2
A: Maltose-binding periplasmic protein
H: sAB Heavy Chain
L: sAB Light Chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,30114
ポリマ－93,2583
非ポリマー1,04211
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-81 kcal/mol
Surface area33290 Å2
手法PISA
単位格子
Length a, b, c (Å)217.170, 42.380, 200.660
Angle α, β, γ (deg.)90.000, 90.070, 90.000
Int Tables number5
Space group name H-MC121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain C and (resid 3 through 19 or resid 21...
21(chain H and (resid 3 through 19 or resid 21...
12(chain A and (resid 1 through 41 or resid 43...
22(chain B and (resid 1 through 41 or resid 43...
13(chain D and (resid 1 through 10 or resid 12...
23(chain L and (resid 1 through 10 or resid 12...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERGLYGLY(chain C and (resid 3 through 19 or resid 21...CC3 - 193 - 19
121LEULEUASPASP(chain C and (resid 3 through 19 or resid 21...CC21 - 7621 - 76
131SERSERTYRTYR(chain C and (resid 3 through 19 or resid 21...CC78 - 9878 - 98
141ALAALAGLYGLY(chain C and (resid 3 through 19 or resid 21...CC100 - 155100 - 155
151LEULEUVALVAL(chain C and (resid 3 through 19 or resid 21...CC157 - 168157 - 168
161TRPTRPLEULEU(chain C and (resid 3 through 19 or resid 21...CC170 - 194170 - 194
171SERSERVALVAL(chain C and (resid 3 through 19 or resid 21...CC196 - 214196 - 214
181HISHISPROPRO(chain C and (resid 3 through 19 or resid 21...CC216 - 229216 - 229
211SERSERGLYGLY(chain H and (resid 3 through 19 or resid 21...HD3 - 193 - 19
221LEULEUASPASP(chain H and (resid 3 through 19 or resid 21...HD21 - 7621 - 76
231SERSERTYRTYR(chain H and (resid 3 through 19 or resid 21...HD78 - 9878 - 98
241ALAALASERSER(chain H and (resid 3 through 19 or resid 21...HD100 - 143100 - 143
251THRTHRGLYGLY(chain H and (resid 3 through 19 or resid 21...HD151 - 155151 - 155
261LEULEUVALVAL(chain H and (resid 3 through 19 or resid 21...HD157 - 168157 - 168
271TRPTRPLEULEU(chain H and (resid 3 through 19 or resid 21...HD170 - 194170 - 194
281SERSERVALVAL(chain H and (resid 3 through 19 or resid 21...HD196 - 214196 - 214
291HISHISPROPRO(chain H and (resid 3 through 19 or resid 21...HD216 - 229216 - 229
112LYSLYSASPASP(chain A and (resid 1 through 41 or resid 43...AB1 - 4132 - 72
122LEULEUASPASP(chain A and (resid 1 through 41 or resid 43...AB43 - 13674 - 167
132GLUGLUPHEPHE(chain A and (resid 1 through 41 or resid 43...AB138 - 169169 - 200
142TYRTYRGLYGLY(chain A and (resid 1 through 41 or resid 43...AB171 - 174202 - 205
152LYSLYSLYSLYS(chain A and (resid 1 through 41 or resid 43...AB175206
162LYSLYSASNASN(chain A and (resid 1 through 41 or resid 43...AB1 - 36732 - 398
172LYSLYSASNASN(chain A and (resid 1 through 41 or resid 43...AB1 - 36732 - 398
182LYSLYSASNASN(chain A and (resid 1 through 41 or resid 43...AB1 - 36732 - 398
192LYSLYSASNASN(chain A and (resid 1 through 41 or resid 43...AB1 - 36732 - 398
212LYSLYSASPASP(chain B and (resid 1 through 41 or resid 43...BA1 - 4132 - 72
222LEULEUASPASP(chain B and (resid 1 through 41 or resid 43...BA43 - 13674 - 167
232GLUGLUPHEPHE(chain B and (resid 1 through 41 or resid 43...BA138 - 169169 - 200
242TYRTYRALAALA(chain B and (resid 1 through 41 or resid 43...BA171 - 312202 - 343
252ASPASPLEULEU(chain B and (resid 1 through 41 or resid 43...BA314 - 361345 - 392
262LYSLYSLYSLYS(chain B and (resid 1 through 41 or resid 43...BA362393
272LYSLYSASNASN(chain B and (resid 1 through 41 or resid 43...BA1 - 36732 - 398
282LYSLYSASNASN(chain B and (resid 1 through 41 or resid 43...BA1 - 36732 - 398
292LYSLYSASNASN(chain B and (resid 1 through 41 or resid 43...BA1 - 36732 - 398
2102LYSLYSASNASN(chain B and (resid 1 through 41 or resid 43...BA1 - 36732 - 398
2112LYSLYSASNASN(chain B and (resid 1 through 41 or resid 43...BA1 - 36732 - 398
2122LYSLYSASNASN(chain B and (resid 1 through 41 or resid 43...BA1 - 36732 - 398
113SERSERSERSER(chain D and (resid 1 through 10 or resid 12...DE1 - 101 - 10
123LEULEULEULEU(chain D and (resid 1 through 10 or resid 12...DE1212
133ALAALAGLYGLY(chain D and (resid 1 through 10 or resid 12...DE14 - 6514 - 65
143ARGARGGLNGLN(chain D and (resid 1 through 10 or resid 12...DE67 - 15767 - 157
153GLYGLYTHRTHR(chain D and (resid 1 through 10 or resid 12...DE159 - 166159 - 166
163GLNGLNALAALA(chain D and (resid 1 through 10 or resid 12...DE168 - 195168 - 195
173GLUGLUSERSER(chain D and (resid 1 through 10 or resid 12...DE197 - 204197 - 204
183PROPROCYSCYS(chain D and (resid 1 through 10 or resid 12...DE206 - 216206 - 216
213SERSERSERSER(chain L and (resid 1 through 10 or resid 12...LF1 - 101 - 10
223LEULEULEULEU(chain L and (resid 1 through 10 or resid 12...LF1212
233ALAALAGLYGLY(chain L and (resid 1 through 10 or resid 12...LF14 - 6514 - 65
243ARGARGGLNGLN(chain L and (resid 1 through 10 or resid 12...LF67 - 15767 - 157
253GLYGLYTHRTHR(chain L and (resid 1 through 10 or resid 12...LF159 - 166159 - 166
263GLNGLNALAALA(chain L and (resid 1 through 10 or resid 12...LF168 - 195168 - 195
273GLUGLUSERSER(chain L and (resid 1 through 10 or resid 12...LF197 - 204197 - 204
283PROPROCYSCYS(chain L and (resid 1 through 10 or resid 12...LF206 - 216206 - 216

NCSアンサンブル:
ID
1
2
3

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要素

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抗体 , 2種, 4分子 CHDL

#2: 抗体 sAB Heavy Chain


分子量: 25478.369 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pRH2.2 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21
#3: 抗体 sAB Light Chain


分子量: 23604.180 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pRH2.2 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21

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タンパク質 / 糖 , 2種, 4分子 BA

#1: タンパク質 Maltose-binding periplasmic protein / MBP / MMBP / Maltodextrin-binding protein


分子量: 44175.613 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 株: K12 / 遺伝子: malE, b4034, JW3994 / プラスミド: pHFT2 / 詳細 (発現宿主): N-terminal 10xHis, Flag, TEV / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P0AEX9
#4: 多糖 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


タイプ: oligosaccharide, Oligosaccharide / クラス: 栄養素 / 分子量: 342.297 Da / 分子数: 2 / 由来タイプ: 組換発現 / 詳細: oligosaccharide / 参照: alpha-maltose
記述子タイププログラム
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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非ポリマー , 4種, 243分子

#5: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 7 / 由来タイプ: 合成 / 式: Cl
#6: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 11 / 由来タイプ: 合成 / 式: C3H8O3
#7: 化合物
ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 4 / 由来タイプ: 合成 / 式: PO4
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 221 / 由来タイプ: 天然 / 式: H2O

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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: 2.58 Å3/Da / 溶媒含有率: 52.34 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.2 M KSCN and 18% PEG 3350

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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: APS / ビームライン: 24-ID-C / 波長: 0.9791 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2015年5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: 0.9791 Å / 相対比: 1
反射解像度: 2.6→19.938 Å / Num. obs: 57286 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / 冗長度: 6.514 % / Biso Wilson estimate: 44.42 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.218 / Χ2: 0.944 / Net I/σ(I): 8.41
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.76.9561.381.7460820.6311.49100
2.7-2.86.8891.0772.1952530.7131.165100
2.8-2.96.8290.8352.8545340.8020.90499.9
2.9-36.5850.6463.4539880.8520.70199.8
3-46.5090.2846.94214260.9710.30999.6
4-55.5160.08515.675920.9920.09598
5-66.9450.08618.0935000.9960.09399.8
6-106.5630.07319.7538010.9970.07999.8
10-156.5670.05626.167670.9980.06199.4
15-205.7680.06621.881980.9960.07298.5
19.938-204.80.0522.321450.9970.05589

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解析

ソフトウェア
名称バージョン分類
XSCALEデータスケーリング
PHENIX精密化
PDB_EXTRACT3.22データ抽出
MD2データ収集
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3PGF

3pgf


解像度: 2.6→19.938 Å / SU ML: 0.33 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.45
Rfactor反射数%反射
Rfree0.2588 2864 5.01 %
Rwork0.2121 --
obs0.2144 57135 99.53 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 159.3 Å2 / Biso mean: 53.9958 Å2 / Biso min: 18.61 Å2
精密化ステップサイクル: final / 解像度: 2.6→19.938 Å
タンパク質核酸リガンド溶媒全体
原子数12388 0 139 223 12750
Biso mean--56.7 43.22 -
残基数----1614
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00312957
X-RAY DIFFRACTIONf_angle_d0.54317659
X-RAY DIFFRACTIONf_chiral_restr0.0431947
X-RAY DIFFRACTIONf_plane_restr0.0042238
X-RAY DIFFRACTIONf_dihedral_angle_d12.6087758
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11C1857X-RAY DIFFRACTION7.695TORSIONAL
12H1857X-RAY DIFFRACTION7.695TORSIONAL
21A3358X-RAY DIFFRACTION7.695TORSIONAL
22B3358X-RAY DIFFRACTION7.695TORSIONAL
31D1910X-RAY DIFFRACTION7.695TORSIONAL
32L1910X-RAY DIFFRACTION7.695TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.64480.33871990.293726692868100
2.6448-2.69270.32651790.293626352814100
2.6927-2.74440.33981390.276126482787100
2.7444-2.80030.33171130.275327592872100
2.8003-2.8610.31281440.266927182862100
2.861-2.92730.27451260.254426872813100
2.9273-3.00030.28851390.240427072846100
3.0003-3.08110.27981700.251826522822100
3.0811-3.17150.24121510.227126802831100
3.1715-3.27340.28181150.214527662881100
3.2734-3.38990.26711360.21326742810100
3.3899-3.52490.25261250.191127742899100
3.5249-3.68430.27181040.189327232827100
3.6843-3.87720.27131370.19382736287399
3.8772-4.11820.23991620.1932606276898
4.1182-4.43290.21991250.18722676280198
4.4329-4.87310.23571540.18642709286398
4.8731-5.56480.22141420.204927602902100
5.5648-6.96110.28331760.22828012977100
6.9611-19.93890.21021280.186428913019100
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)
16.5692.26692.85192.61271.91872.2858-0.29411.1356-1.2065-0.63580.04960.17560.9691-1.0022-0.060.6907-0.3245-0.08260.9671-0.19070.7266-44.685-0.56161.567
22.4532-0.1678-0.56880.78930.15443.3956-0.06750.32110.0851-0.05420.10210.23270.0808-0.6725-0.0330.2916-0.0192-0.03620.4190.01630.4673-39.30914.33678.208
36.9455-2.0192.16133.96640.22855.38630.2711-0.06370.7439-0.0724-0.38220.4351-1.4173-1.30440.2730.81390.16950.19530.5261-0.0060.6719-37.43330.08823.191
44.9754-0.78610.76141.37150.90664.66910.0934-0.19330.51660.2748-0.01460.41560.0806-1.0198-0.06840.5077-0.02910.1030.45130.0140.3954-32.8514.58228.179
53.16650.4499-0.93251.25930.24884.4053-0.20350.9194-0.2035-0.26110.25720.199-0.1012-0.5033-0.110.456-0.11810.03230.6288-0.05860.4172-26.63411.578-3.837
62.70130.26910.11590.8549-0.17634.4764-0.07350.4115-0.3220.05460.2671-0.06120.31410.307-0.16190.5044-0.07590.03910.3601-0.09160.4182-18.2966.7448.152
73.4559-0.1134-0.52171.74980.77615.1165-0.0260.61270.0595-0.11110.06170.1978-0.0555-0.7841-0.10170.3683-0.06590.03070.50910.06950.3466-31.29214.3556.134
83.20810.0553-0.13851.81240.76914.9192-0.04020.17940.10020.0171-0.00940.39850.067-1.33840.10450.4184-0.05340.08520.73090.0760.5028-41.73414.48316.066
95.4139-0.8968-2.33080.62852.22567.89-0.07440.1803-0.0220.11540.5271-0.3760.260.7663-0.34970.459-0.017-0.00930.4574-0.11780.4335-10.719.65514.229
103.4308-0.2102-5.34841.8-0.66768.8672-0.1692-0.1054-0.41060.1788-0.0024-0.10820.08030.40330.62170.27490.0721-0.02610.55620.09150.442229.688-20.20580.855
114.3131-1.0147-5.77891.12551.09157.83070.36870.0499-0.2753-0.1249-0.39460.0948-0.52390.25570.03190.35680.0287-0.06150.31560.06250.375722.453-13.39688.637
129.48283.64693.0993.51121.19074.59920.1203-1.20860.69790.6637-0.577-0.4322-0.67350.12840.46040.6049-0.136-0.08730.36210.01650.508729.633-7.37786.233
137.045-0.1053-2.45740.4758-0.83654.5942-0.2747-0.50110.14840.08770.0781-0.226-0.14460.69140.190.3287-0.0435-0.03110.3067-0.01570.419124.815-14.60187.744
146.19442.5549-6.2322.9237-1.10287.4563-0.8891-1.1115-1.4333-0.13330.4658-0.06990.53741.07511.06280.4330.1891-0.0620.66260.12750.490735.752-21.589.103
155.07230.567-0.48482.9583-0.30464.32310.3326-0.10570.3161-0.0030.6114-0.0631-1.0421.3320.28590.5746-0.34520.06731.0021-0.00630.509240.09238.437.879
166.12491.12351.29581.65040.81366.2432-0.34630.45850.4364-0.3768-0.30880.152-0.14341.06960.06620.6551-0.01240.06450.72630.00550.412733.33133.60927.308
174.82330.8368-1.66722.5861-0.98641.768-0.5009-0.1754-0.9967-0.4984-0.7504-1.1898-0.11891.25180.32110.53280.00840.12971.01110.08110.649344.90125.64531.349
182.86530.4964-0.74092.5384-0.92873.6977-0.01470.8007-0.4536-0.26010.0822-0.6584-0.20131.41060.1970.4525-0.14230.07790.8585-0.03450.339737.09632.40229.986
192.6545-1.3532-1.03043.264-3.13095.61690.0961-0.45870.02660.6428-0.3014-0.983-1.12781.66710.52460.5769-0.4280.08561.67370.18340.881449.34238.74333.429
207.71611.8971-2.17291.9896-1.35833.4134-0.05080.0223-1.0512-0.2896-0.1279-0.49180.1134-0.06280.10730.46030.03630.0290.1613-0.02620.37272.302-5.36259.082
214.0903-1.5279-1.00764.13710.32061.3312-0.01540.4551-0.1858-0.1219-0.0010.14390.268-0.14020.01070.2935-0.008-0.01620.1589-0.01070.2995-7.231-2.09560.064
224.99712.75060.29174.86060.97176.37790.04780.16370.40150.1179-0.2349-0.64910.21710.95490.15510.20370.022-0.00490.2507-0.0190.2536-0.7113.41168.678
232.6974-0.5420.52911.53730.90651.267-0.06730.03270.116-0.19340.002-0.0371-0.1571-0.07750.06480.4295-0.00010.00310.20970.03220.3207-2.4484.08959.518
243.8514-2.25080.14091.5704-0.36060.1889-0.09090.1106-0.15070.1939-0.01120.05280.0804-0.02130.09530.4258-0.0279-0.07250.2116-0.03290.3191-1.506-2.20866.637
256.32810.2896-1.54353.98822.29693.15930.2905-1.0221-0.6660.6478-0.4867-0.39130.57791.24170.16710.4098-0.018-0.1330.37690.06280.375524.466-23.47580.33
262.4706-1.47230.77251.12470.56765.95280.013-0.0540.1885-0.08290.05160.4286-0.0702-0.0025-0.06770.31430.02580.00320.16580.04960.265716.662-17.06972.718
273.45160.7396-0.76134.7691-6.39388.80110.3869-0.3332-0.44140.33550.1357-0.19840.4121-0.0347-0.33340.4396-0.0678-0.1160.29070.12970.399219.812-24.93779.605
285.6384-0.2594-0.15668.3444-3.61082.4304-0.02180.25-0.45260.4546-0.2676-0.2416-0.35910.16330.20570.40260.0247-0.01940.1712-0.00070.32718.425-25.90968.66
295.1512-0.73752.23265.8752-3.9085.21870.0346-0.30870.0376-0.1678-0.132-1.3390.826-0.2111-0.0550.38830.0147-0.08050.292-0.02420.500924.534-26.92368.722
305.20390.0322.66081.58383.13727.5126-0.20010.85541.4509-0.5846-0.6222-0.2918-0.8458-0.33950.35140.65860.01160.1340.32890.12370.5658-3.17535.68838.936
318.0903-1.32964.33392.1253-0.67755.00640.3615-0.4674-0.0155-0.163-0.1380.04220.1376-0.502-0.13620.43680.04310.04050.148-0.01680.2413-0.51626.50946.53
324.6016-0.5641.58184.11440.23255.0348-0.00570.966-0.8775-0.28150.061-0.7361-0.36430.7369-0.02620.3991-0.0122-0.01140.365-0.05170.38995.37322.21636.882
334.58690.92230.54141.1073-0.07412.60410.15490.108-0.50160.1053-0.0672-0.17360.0416-0.05040.05280.5410.03070.0070.1454-0.03880.411-4.16119.09743.83
344.14590.98682.14991.14320.48883.19260.53460.5539-0.3813-0.4441-0.25830.1330.53670.2953-0.20930.5899-0.0404-0.04270.3204-0.01890.28285.54921.07542.025
352.04080.73791.38010.35710.82981.95430.15870.1327-0.3089-0.2288-0.1018-0.26020.0780.432-0.0520.60620.02310.03010.27880.01210.4285-14.33217.83929.627
363.63640.35453.70291.3040.86574.7078-0.02710.13040.00170.0327-0.12940.4612-0.44970.01040.23070.4872-0.00780.01260.24220.05690.32323.32527.51737.298
372.7151-0.53781.37162.20681.49853.73730.0657-0.01750.28540.15380.0355-0.1069-0.26841.2734-0.1470.2709-0.0454-0.04090.4357-0.04140.376630.43534.98546.894
385.11072.7313-0.63372.768-2.03395.3048-0.01990.73780.2775-0.3020.3267-0.0956-0.3746-0.1635-0.23250.4674-0.07050.01420.37020.01370.382928.19736.44141.948
393.49280.43090.34983.0909-1.99024.9554-0.04590.47580.3711-0.61530.25920.1609-0.49380.1986-0.21580.6003-0.11810.03550.34970.10560.349926.55938.87437.649
402.04940.85140.34722.4341-1.46691.3031-0.28630.24170.9831-0.15920.38310.0347-1.55240.54390.01081.1884-0.5069-0.0251.20250.31761.298434.85856.36433.666
412.95671.3483-0.73393.2528-3.54084.24760.10720.55650.7199-0.34420.1430.1473-1.79880.0813-0.29160.7635-0.12940.09560.34160.03820.391726.43644.42846.521
424.05960.06560.20155.6195-2.36355.2858-0.3801-0.66260.4808-0.09290.2916-0.92510.25240.4465-0.00440.36640.0942-0.04280.4649-0.11520.2763-3.142-0.02388.309
433.8576-0.1091-0.07851.3977-1.9953.1399-0.1371-0.29230.00280.40210.21360.0345-0.0868-0.0189-0.10620.33230.0124-0.00760.2056-0.03560.2761-11.333-0.84982.924
441.89252.7148-0.75717.3302-5.28165.4048-0.0189-0.4295-0.2833-0.0656-0.00630.19790.3670.27760.03480.33750.15440.04320.38660.020.3592-6.494-7.68584.494
453.3526-0.3071-0.07010.8482-1.35412.1503-0.3510.09610.39340.30920.1470.2076-0.43750.09180.24730.3299-0.013-0.09290.2203-0.05160.3841-7.4058.85176.144
462.35890.58331.44023.4814-3.42155.19980.7758-0.10610.1261-0.8794-0.6156-0.07930.26090.4901-0.18650.3970.1171-0.00790.2972-0.01690.33023.734-13.59193.71
472.00671.9254-0.17529.44742.16343.6740.0218-0.5351-0.92890.5775-0.4306-0.26-0.13570.2829-0.11840.54720.1337-0.11030.8298-0.18470.45256.44610.72524.787
484.14672.9218-0.75316.4317-0.50710.1764-0.06361.4114-0.3256-0.2770.3791-0.253-0.07790.0086-0.26730.7001-0.02780.02760.7753-0.07780.305811.91323.93313.619
494.0443-0.6788-1.23121.6636-0.07885.1325-0.36120.918-0.6267-0.52120.5352-0.2755-0.25080.32940.1150.5282-0.01770.00150.3915-0.11070.37340.6517.77822.35
502.880.5075-1.19561.9215-0.64581.13680.0680.23760.41270.47480.4382-0.2156-0.53380.68560.0380.4745-0.091-0.04280.6196-0.14450.18684.88930.63326.659
514.74251.6824-1.11551.337-0.92414.06970.34170.99390.393-0.1542-0.30850.0798-0.0526-0.4074-0.16980.57520.0361-0.05650.5352-0.00160.386-4.06329.26117.817
527.60960.1528-1.22710.41431.09263.1861-0.45011.3095-1.23020.01090.3805-0.1931-0.21620.2040.08070.6206-0.08310.04670.7197-0.19620.26591.98120.01312.938
534.34831.798-2.5473.2132-0.23855.55060.24071.21540.4691-0.10110.1302-0.3224-1.0780.6685-0.25210.9335-0.1884-0.01320.9003-0.02410.50269.57735.0315.168
542.7679-1.2433-0.87541.6142-1.0742.33110.13510.2363-0.7112-0.11470.21280.3687-0.07081.00390.07950.5375-0.1624-0.04920.5039-0.16540.30275.34621.53524.372
556.67280.7556-1.35081.18950.12195.4878-0.5319-0.1239-0.5143-0.47140.4235-0.15590.91080.18670.16280.51330.05390.00570.294-0.08190.47860.54513.88527.409
563.6390.4473-1.35081.526-0.31640.5168-0.59451.2805-0.4405-0.5247-0.05780.2351-0.7788-0.4695-0.01660.7266-0.30580.01920.88730.06810.268921.19733.14515.402
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 1:42 )B1 - 42
2X-RAY DIFFRACTION2( CHAIN B AND RESID 43:367 )B43 - 367
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1:42 )A1 - 42
4X-RAY DIFFRACTION4( CHAIN A AND RESID 43:105 )A43 - 105
5X-RAY DIFFRACTION5( CHAIN A AND RESID 106:153 )A106 - 153
6X-RAY DIFFRACTION6( CHAIN A AND RESID 154:218 )A154 - 218
7X-RAY DIFFRACTION7( CHAIN A AND RESID 219:272 )A219 - 272
8X-RAY DIFFRACTION8( CHAIN A AND RESID 273:333 )A273 - 333
9X-RAY DIFFRACTION9( CHAIN A AND RESID 334:367 )A334 - 367
10X-RAY DIFFRACTION10( CHAIN D AND RESID 113:130 )D113 - 130
11X-RAY DIFFRACTION11( CHAIN D AND RESID 131:152 )D131 - 152
12X-RAY DIFFRACTION12( CHAIN D AND RESID 153:165 )D153 - 165
13X-RAY DIFFRACTION13( CHAIN D AND RESID 166:206 )D166 - 206
14X-RAY DIFFRACTION14( CHAIN D AND RESID 207:216 )D207 - 216
15X-RAY DIFFRACTION15( CHAIN L AND RESID 113:130 )L113 - 130
16X-RAY DIFFRACTION16( CHAIN L AND RESID 131:146 )L131 - 146
17X-RAY DIFFRACTION17( CHAIN L AND RESID 147:160 )L147 - 160
18X-RAY DIFFRACTION18( CHAIN L AND RESID 161:206 )L161 - 206
19X-RAY DIFFRACTION19( CHAIN L AND RESID 207:216 )L207 - 216
20X-RAY DIFFRACTION20( CHAIN C AND RESID 3:20 )C3 - 20
21X-RAY DIFFRACTION21( CHAIN C AND RESID 21:42 )C21 - 42
22X-RAY DIFFRACTION22( CHAIN C AND RESID 43:55 )C43 - 55
23X-RAY DIFFRACTION23( CHAIN C AND RESID 56:102 )C56 - 102
24X-RAY DIFFRACTION24( CHAIN C AND RESID 103:140 )C103 - 140
25X-RAY DIFFRACTION25( CHAIN C AND RESID 141:161 )C141 - 161
26X-RAY DIFFRACTION26( CHAIN C AND RESID 162:191 )C162 - 191
27X-RAY DIFFRACTION27( CHAIN C AND RESID 192:205 )C192 - 205
28X-RAY DIFFRACTION28( CHAIN C AND RESID 206:219 )C206 - 219
29X-RAY DIFFRACTION29( CHAIN C AND RESID 220:230 )C220 - 230
30X-RAY DIFFRACTION30( CHAIN H AND RESID 3:10 )H3 - 10
31X-RAY DIFFRACTION31( CHAIN H AND RESID 11:35 )H11 - 35
32X-RAY DIFFRACTION32( CHAIN H AND RESID 36:47 )H36 - 47
33X-RAY DIFFRACTION33( CHAIN H AND RESID 48:86 )H48 - 86
34X-RAY DIFFRACTION34( CHAIN H AND RESID 87:102 )H87 - 102
35X-RAY DIFFRACTION35( CHAIN H AND RESID 103:113 )H103 - 113
36X-RAY DIFFRACTION36( CHAIN H AND RESID 114:127 )H114 - 127
37X-RAY DIFFRACTION37( CHAIN H AND RESID 128:143 )H128 - 143
38X-RAY DIFFRACTION38( CHAIN H AND RESID 151:166 )H151 - 166
39X-RAY DIFFRACTION39( CHAIN H AND RESID 167:200 )H167 - 200
40X-RAY DIFFRACTION40( CHAIN H AND RESID 201:209 )H201 - 209
41X-RAY DIFFRACTION41( CHAIN H AND RESID 210:229 )H210 - 229
42X-RAY DIFFRACTION42( CHAIN D AND RESID 1:19 )D1 - 19
43X-RAY DIFFRACTION43( CHAIN D AND RESID 20:76 )D20 - 76
44X-RAY DIFFRACTION44( CHAIN D AND RESID 77:91 )D77 - 91
45X-RAY DIFFRACTION45( CHAIN D AND RESID 92:104 )D92 - 104
46X-RAY DIFFRACTION46( CHAIN D AND RESID 105:112 )D105 - 112
47X-RAY DIFFRACTION47( CHAIN L AND RESID 1:8 )L1 - 8
48X-RAY DIFFRACTION48( CHAIN L AND RESID 9:26 )L9 - 26
49X-RAY DIFFRACTION49( CHAIN L AND RESID 27:39 )L27 - 39
50X-RAY DIFFRACTION50( CHAIN L AND RESID 40:49 )L40 - 49
51X-RAY DIFFRACTION51( CHAIN L AND RESID 50:62 )L50 - 62
52X-RAY DIFFRACTION52( CHAIN L AND RESID 63:76 )L63 - 76
53X-RAY DIFFRACTION53( CHAIN L AND RESID 77:85 )L77 - 85
54X-RAY DIFFRACTION54( CHAIN L AND RESID 86:91 )L86 - 91
55X-RAY DIFFRACTION55( CHAIN L AND RESID 92:104 )L92 - 104
56X-RAY DIFFRACTION56( CHAIN L AND RESID 105:112 )L105 - 112

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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