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- PDB-6x3m: Crystal structure of full-length Streptococcal bacteriophage hyal... -

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基本情報

登録情報
データベース: PDB / ID: 6x3m
タイトルCrystal structure of full-length Streptococcal bacteriophage hyaluronidase in complex with unsaturated hyaluronan octa-saccharides
要素Hyaluronoglucosaminidase
キーワードLYASE / HylP / Hyaluronidase / S. pyogenes phage H4489A / Beta-elimination / unsaturated Hyaluronan Octa-saccharides
機能・相同性
機能・相同性情報


symbiont entry into host cell via disruption of host cell glycocalyx / hyaluronoglucosaminidase / hyalurononglucosaminidase activity / capsule polysaccharide biosynthetic process / symbiont entry into host cell via disruption of host cell envelope / virion component
類似検索 - 分子機能
Hyaluronidase, bacterial / Hyaluronidase protein (HylP) / Major tropism determinant, N-terminal domain / Major tropism determinant N-terminal domain
類似検索 - ドメイン・相同性
Hyaluronoglucosaminidase
類似検索 - 構成要素
生物種Streptococcus pyogenes phage H4489A (ファージ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.581 Å
データ登録者Deivanayagam, C. / Schormann, N.
引用ジャーナル: To Be Published
タイトル: Crystal Structure of Streptococcal Bacteriophage Hyaluronidase: Presence of a Prokaryotic Collagen and Elucidation of Catalytic Mechanism
著者: Lee, J.H. / Schormann, N. / Rajashankar, K.R. / Deivanaygam, C.
履歴
登録2020年5月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年6月9日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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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: Hyaluronoglucosaminidase
B: Hyaluronoglucosaminidase
C: Hyaluronoglucosaminidase
D: Hyaluronoglucosaminidase
E: Hyaluronoglucosaminidase
F: Hyaluronoglucosaminidase
G: Hyaluronoglucosaminidase
H: Hyaluronoglucosaminidase
I: Hyaluronoglucosaminidase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)386,28527
ポリマ－365,8029
非ポリマー20,48318
水00
1
A: Hyaluronoglucosaminidase
B: Hyaluronoglucosaminidase
C: Hyaluronoglucosaminidase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)128,7629
ポリマ－121,9343
非ポリマー6,8286
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area75080 Å2
ΔGint-175 kcal/mol
Surface area45780 Å2
手法PISA
2
D: Hyaluronoglucosaminidase
E: Hyaluronoglucosaminidase
F: Hyaluronoglucosaminidase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)128,7629
ポリマ－121,9343
非ポリマー6,8286
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area74740 Å2
ΔGint-170 kcal/mol
Surface area46110 Å2
手法PISA
3
G: Hyaluronoglucosaminidase
H: Hyaluronoglucosaminidase
I: Hyaluronoglucosaminidase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)128,7629
ポリマ－121,9343
非ポリマー6,8286
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area75950 Å2
ΔGint-160 kcal/mol
Surface area45340 Å2
手法PISA
単位格子
Length a, b, c (Å)338.168, 56.797, 276.954
Angle α, β, γ (deg.)90.000, 126.680, 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 A and (resid 8 through 234 or resid 236...
21(chain B and (resid 8 through 234 or resid 236...
31(chain C and (resid 8 through 234 or resid 236...
41(chain D and (resid 8 through 234 or resid 236 through 346 or resid 348 through 356))
51(chain E and (resid 8 through 234 or resid 236 through 351 or resid 353 through 356))
61(chain F and (resid 8 through 234 or resid 236...
71(chain G and (resid 8 through 234 or resid 236...
81(chain H and (resid 8 through 346 or resid 348 through 351 or resid 353 through 356))
91(chain I and (resid 8 through 234 or resid 236...

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLEULEU(chain A and (resid 8 through 234 or resid 236...AA8 - 2348 - 234
12ILEILETHRTHR(chain A and (resid 8 through 234 or resid 236...AA236 - 346236 - 346
13GLYGLYGLYGLY(chain A and (resid 8 through 234 or resid 236...AA348348
21ARGARGLEULEU(chain B and (resid 8 through 234 or resid 236...BB8 - 2348 - 234
22ILEILETHRTHR(chain B and (resid 8 through 234 or resid 236...BB236 - 346236 - 346
23PROPROLEULEU(chain B and (resid 8 through 234 or resid 236...BB6 - 3676 - 367
31ARGARGLEULEU(chain C and (resid 8 through 234 or resid 236...CC8 - 2348 - 234
32ILEILETHRTHR(chain C and (resid 8 through 234 or resid 236...CC236 - 346236 - 346
33GLYGLYGLYGLY(chain C and (resid 8 through 234 or resid 236...CC348348
41ARGARGLEULEU(chain D and (resid 8 through 234 or resid 236 through 346 or resid 348 through 356))DD8 - 2348 - 234
42ILEILETHRTHR(chain D and (resid 8 through 234 or resid 236 through 346 or resid 348 through 356))DD236 - 346236 - 346
43GLYGLYTYRTYR(chain D and (resid 8 through 234 or resid 236 through 346 or resid 348 through 356))DD348 - 356348 - 356
51ARGARGLEULEU(chain E and (resid 8 through 234 or resid 236 through 351 or resid 353 through 356))EE8 - 2348 - 234
52ILEILEALAALA(chain E and (resid 8 through 234 or resid 236 through 351 or resid 353 through 356))EE236 - 351236 - 351
53THRTHRTYRTYR(chain E and (resid 8 through 234 or resid 236 through 351 or resid 353 through 356))EE353 - 356353 - 356
61ARGARGLEULEU(chain F and (resid 8 through 234 or resid 236...FF8 - 2348 - 234
62ILEILETHRTHR(chain F and (resid 8 through 234 or resid 236...FF236 - 346236 - 346
63GLYGLYALAALA(chain F and (resid 8 through 234 or resid 236...FF348 - 351348 - 351
64THRTHRTYRTYR(chain F and (resid 8 through 234 or resid 236...FF353 - 356353 - 356
71ARGARGLEULEU(chain G and (resid 8 through 234 or resid 236...GG8 - 2348 - 234
72ILEILETHRTHR(chain G and (resid 8 through 234 or resid 236...GG236 - 346236 - 346
73GLYGLYGLYGLY(chain G and (resid 8 through 234 or resid 236...GG348348
81ARGARGTHRTHR(chain H and (resid 8 through 346 or resid 348 through 351 or resid 353 through 356))HH8 - 3468 - 346
82GLYGLYALAALA(chain H and (resid 8 through 346 or resid 348 through 351 or resid 353 through 356))HH348 - 351348 - 351
83THRTHRTYRTYR(chain H and (resid 8 through 346 or resid 348 through 351 or resid 353 through 356))HH353 - 356353 - 356
91ARGARGLEULEU(chain I and (resid 8 through 234 or resid 236...II8 - 2348 - 234
92ILEILETHRTHR(chain I and (resid 8 through 234 or resid 236...II236 - 346236 - 346
93PROPROLEULEU(chain I and (resid 8 through 234 or resid 236...II6 - 3676 - 367

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要素

#1: タンパク質
Hyaluronoglucosaminidase / Hyaluronidase


分子量: 40644.656 Da / 分子数: 9 / 由来タイプ: 組換発現
由来: (組換発現) Streptococcus pyogenes phage H4489A (ファージ)
遺伝子: HYLP1, HYLP / プラスミド: pET24a / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P15316, hyaluronate lyase
#2: 多糖
4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 758.633 Da / 分子数: 9 / 由来タイプ: 組換発現
記述子タイププログラム
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2122A-1b_1-5][a21eEA-1a_1-5]/1-2-1-3/a3-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-4-deoxy-GlcpA]{}}}}LINUCSPDB-CARE
#3: 多糖
4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1517.267 Da / 分子数: 9 / 由来タイプ: 組換発現
記述子タイププログラム
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a2122A-1b_1-5][a21eEA-1a_1-5]/1-2-1-2-1-2-1-3/a3-b1_b4-c1_c3-d1_d4-e1_e3-f1_f4-g1_g3-h1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-4-deoxy-IdopA]{}}}}}}}}LINUCSPDB-CARE
研究の焦点であるリガンドがあるかY

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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: 2.92 Å3/Da / 溶媒含有率: 57.81 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5
詳細: 17.5-18.5% (w/v) PEG 2000 MME, 70 mM KBr, 62.5 mM Glycine, 100 mM Tris-HCl, pH 8.5; prior to crystallization the protein was incubated with unsaturated hyaluronan octa-saccharides at a molar ratio of 1:50

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
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-E / 波長: 0.97918 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2012年5月29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: 0.97918 Å / 相対比: 1
反射解像度: 3.581→35 Å / Num. obs: 49298 / % possible obs: 97.5 % / 冗長度: 4.2 % / Biso Wilson estimate: 91.96 Å2 / Rmerge(I) obs: 0.124 / Χ2: 1.537 / Net I/av σ(I): 14.4 / Net I/σ(I): 6.5
反射 シェル解像度: 3.6→3.73 Å / 冗長度: 3 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.52 / Num. unique obs: 4295 / Χ2: 1.068 / % possible all: 86.5

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解析

ソフトウェア
名称バージョン分類
PHENIX1.13_2998精密化
SCALEPACKデータスケーリング
PDB_EXTRACT3.25データ抽出
DENZOデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 2C3F, 1BKV

2c3f

1bkv


解像度: 3.581→29.867 Å / SU ML: 0.43 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 30.38 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2991 2519 5.17 %
Rwork0.2473 46186 -
obs0.25 48705 95.83 %
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 max: 230.47 Å2 / Biso mean: 105.6094 Å2 / Biso min: 28.32 Å2
精密化ステップサイクル: final / 解像度: 3.581→29.867 Å
タンパク質核酸リガンド溶媒全体
原子数24172 0 1402 0 25574
Biso mean--96.31 --
残基数----3241
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A9315X-RAY DIFFRACTION9.214TORSIONAL
12B9315X-RAY DIFFRACTION9.214TORSIONAL
13C9315X-RAY DIFFRACTION9.214TORSIONAL
14D9315X-RAY DIFFRACTION9.214TORSIONAL
15E9315X-RAY DIFFRACTION9.214TORSIONAL
16F9315X-RAY DIFFRACTION9.214TORSIONAL
17G9315X-RAY DIFFRACTION9.214TORSIONAL
18H9315X-RAY DIFFRACTION9.214TORSIONAL
19I9315X-RAY DIFFRACTION9.214TORSIONAL
LS精密化 シェル解像度: 3.581→3.6498 Å / Rfactor Rfree error: 0
Rfactor反射数%反射
Rfree0.354 113 -
Rwork0.3234 1907 -
obs--73 %
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)
15.0295-2.7895-0.38163.9134-1.97467.5788-0.0135-0.2486-1.7-0.24940.46140.82960.9545-1.1019-0.35111.0866-0.1954-0.03330.4360.13630.8549-16.1249-40.1061111.352
23.2092-0.1436-0.40325.1518-5.32097.1834-0.1498-0.0701-0.5110.19720.21030.76430.0255-0.741-0.04070.4951-0.0779-0.07630.7501-0.06690.5576-17.7003-32.582699.5699
30.1221-0.63871.29431.3614-3.42387.3368-0.19890.08890.11380.2223-0.0745-0.0659-0.3305-0.00830.14710.6403-0.0094-0.19090.82680.10870.5342-28.5149-5.354-18.7302
45.7753-0.84072.53692.4767-3.66578.5301-0.1864-0.72390.43170.59590.0044-1.0544-1.0245-0.80860.05481.0010.0917-0.29730.63050.08310.8207-40.234827.3863-67.4063
53.6601-1.44771.65083.9511-2.30975.88430.159-0.2151-0.40130.00970.06220.51820.4785-1.6034-0.19460.5679-0.1724-0.17030.83950.03590.4587-52.610920.1544-81.6693
64.4835-1.00480.91792.7175-0.61641.20270.01890.41740.1918-0.59360.66230.1320.463-1.1596-0.44130.4527-0.0025-0.16421.46140.27240.4921-59.767934.215-102.7723
70.7603-0.0481-0.42070.09320.22510.67520.01740.78520.69330.01820-0.1113-0.1481-0.05260.01980.8517-0.0899-0.57612.23750.85221.1192-71.961154.45-130.359
80.20740.09210.69550.5219-0.3246.5182-0.0188-0.03960.39090.1055-0.17090.0712-0.7492-0.24040.18570.73740.0233-0.05090.24430.01510.5416-9.2303-24.153682.4211
90.3173-0.54951.68151.4227-3.04937.53130.2926-0.0445-0.1153-0.22780.02220.13650.6835-0.2244-0.37480.556-0.0474-0.1030.75110.22130.6628-31.55421.2695-36.2757
103.3758-0.6252.02512.0553-1.15192.6497-0.337-0.2266-0.2150.14010.64310.3506-0.1229-1.2378-0.31930.4136-0.0399-0.06971.11440.20460.4969-54.865825.846-83.119
110.4711-0.44731.21890.5833-1.08312.7513-0.19551.06870.3947-0.23160.04950.1083-0.0538-0.10650.00940.4604-0.1766-0.33461.98840.68380.8971-63.633441.7345-117.5605
120.1428-0.14670.95020.4209-1.64114.99350.3260.0738-0.0763-0.11330.20230.25170.7023-0.2004-0.40920.99560.1360.04140.3810.07080.5285-10.5549-29.05658.4272
132.2749-0.54332.21781.1309-1.98125.315-0.2130.07420.19230.09660.5230.2687-0.1069-1.3047-0.26970.4636-0.0668-0.15511.00780.24350.5183-54.814929.2025-90.8158
147.66860.23273.25363.23540.60556.64920.2755-1.21490.410.2281-0.61210.611-0.8055-0.74630.28980.7944-0.27270.2180.544-0.05840.6065-14.5809-6.0725185.9468
152.55841.0719-1.65732.4427-0.9085.4992-0.04870.66680.3304-0.3074-0.46020.2086-0.352-1.43590.4870.63550.0722-0.32180.8402-0.01230.7897-15.4445-0.0245173.3798
160.3991-0.51490.141.1085-1.61844.1957-0.098-0.01380.1752-0.1392-0.584-0.2233-0.22670.54920.77091.1352-0.0758-0.06950.7213-0.08160.5772-16.9217.738982.7555
171.34281.24161.16661.8926-1.38768.77460.1152-0.1105-0.10220.3568-0.1891-0.45261.6696-0.57660.07820.6927-0.0542-0.04010.57110.04010.566-39.448622.607220.7435
186.84681.0142.33337.10370.1644.2305-0.64110.0029-0.2655-1.0106-0.1065-0.51290.8359-0.5440.59741.0533-0.12830.18050.76450.14190.4282-45.632534.32360.1175
194.58920.56662.69843.4174-0.62863.799-0.3650.0537-0.5288-0.34250.1642-0.23681.3847-0.99770.230.951-0.33290.12040.7549-0.10710.3109-53.019136.7695-11.658
202.83790.5794-0.53142.4687-1.832.9613-0.79620.40040.3051-0.6914-0.0319-0.08930.9206-0.6422-0.08340.883-0.701-0.21561.5657-0.15910.4546-54.834541.1537-27.0065
211.26581.04710.60611.22440.14041.3942-0.0992-0.08450.0172-0.01670.10380.25840.2709-0.56680.01471.0417-0.8831-0.33651.92390.01260.4989-71.853134.06-27.8187
222.44770.44770.96831.25630.99044.2514-1.19460.71250.9094-0.77530.2830.1792-0.5673-0.06240.41420.8127-0.5655-0.52841.58760.22670.7157-60.709154.929-37.3681
232.08450.5858-0.09732.271-0.0820.7092-0.53431.24010.81140.07760.30090.0522-0.06320.36580.20951.1421-0.6074-0.38882.58580.56630.6186-73.599958.2085-55.0858
244.10851.6702-0.16896.2193.01852.35160.06770.11810.7019-0.1838-0.26051.1588-0.9847-0.25440.2150.9907-0.1207-0.07060.0818-0.05850.6179-6.755810.8155180.7367
250.535-0.20472.05320.2259-1.39497.6564-0.11430.22790.1997-0.184-0.1376-0.13440.59650.39740.15850.99660.00410.02350.88790.01550.4995-16.11219.38991.4051
262.7539-1.9937-0.62822.36320.50262.09960.0840.0902-0.4566-0.4996-0.1906-0.23180.772-0.1829-0.08860.9884-0.1706-0.07960.94690.11410.7961-40.258330.52215.7534
273.00520.57120.74272.0859-1.12674.7478-0.2884-0.32870.2268-0.00340.1124-0.11520.5653-1.15340.21560.7161-0.3953-0.10240.8409-0.01540.4288-54.125939.1465-10.1713
282.37660.50260.43240.9540.27681.0278-0.51170.82450.3542-0.64560.62120.12520.1446-0.8710.6311.2514-1.0729-0.76371.7720.05490.4498-64.919745.2287-32.5493
291.00350.43360.52080.37260.47180.8406-0.0430.1360.1434-0.24060.28890.10780.11750.23210.13761.355-1.1745-1.02482.74180.55561.0341-70.381559.021-61.6372
300.2849-0.52141.11950.2884-1.12863.31690.01160.18590.0239-0.29030.0211-0.05310.5606-0.1659-0.08771.1191-0.163-0.02320.56650.15490.5583-7.6584-0.908134.6984
311.8824-0.06421.751.5637-1.51325.2145-0.33810.20030.1216-0.45660.1837-0.29990.9238-0.98790.01240.7125-0.38150.0530.8027-0.09690.4865-52.539.6303-11.8687
320.0159-0.0146-0.0740.0020.07760.3208-0.23370.1210.226-0.73280.01880.6635-0.0989-0.12410.18841.6514-1.1951-0.71282.26770.33541.2233-75.740654.3958-63.2311
334.55220.35212.07982.50091.56128.0563-0.0192-0.7615-0.9174-0.77970.0839-0.772-0.63650.33760.090.65130.06990.13820.61180.09630.6347-154.4829-6.2611-257.5109
340.49860.0717-1.04940.6178-0.81852.7308-0.50020.1534-0.34310.0017-0.3989-0.34170.7468-0.1490.51270.6019-0.074-0.08820.52390.10210.5843-155.00061.7445-233.7191
350.98581.18431.8442.22013.07256.78690.0852-0.130.3817-0.2483-0.25280.3557-1.2948-0.04830.2291.01880.01570.15320.8644-0.03650.5383-151.370710.473-144.1314
363.5113-0.17262.86621.84761.03373.1023-0.13390.4272-0.1949-0.21370.4852-0.30450.14580.1798-0.37470.9999-0.24850.09920.6354-0.09710.4291-127.393219.3229-79.3387
374.1750.89031.20453.67030.68293.9402-0.2308-0.0670.0892-0.54120.3425-1.08050.04080.5369-0.08640.3255-0.05420.18570.5068-0.15130.6509-113.363625.016-54.214
381.9350.59542.32562.18861.54528.02550.1997-0.48680.05970.21060.122-0.47990.08540.664-0.3130.35490.0057-0.09390.7355-0.11420.6427-103.296329.9516-23.6168
390.28780.10791.60010.04110.88098.67260.0234-0.09140.08490.02410.0817-0.0033-0.50970.161-0.11020.8662-0.139-0.0230.4048-0.02070.4589-152.186911.3182-175.5574
403.14881.11743.65291.54471.26836.4575-0.00670.0096-0.1243-0.06340.1121-0.57430.01860.1886-0.10290.3736-0.03190.0130.4527-0.13440.6993-109.416627.0256-40.0731
415.41540.3989-0.28138.9558-0.35946.59110.27980.1599-0.37730.1181-0.11840.4551-0.19540.5332-0.05580.43520.01320.04270.2782-0.04510.2704-171.7075-5.2413-252.0852
420.2650.09590.87990.60651.93846.4905-0.18090.06630.3590.0874-0.194-0.0157-0.41680.2830.27171.0890.0221-0.00230.1167-0.08610.4914-161.2997-0.3658-210.4798
435.95620.3644.68493.01960.0343.68350.99490.2124-0.44150.1206-0.25860.30463.02180.2301-0.74821.1699-0.02830.12340.52440.06760.3695-148.27154.8175-135.5936
442.29620.51961.54160.23830.11612.02170.06660.37740.149-0.20610.44870.09510.46250.2905-0.45491.4937-0.19450.15060.7407-0.18860.5123-134.402220.0061-89.7876
455.5466-0.38434.22053.99152.00745.33350.42331.2383-1.1577-0.33950.6206-1.18631.08751.4299-1.08520.97390.0945-0.14471.262-0.7490.9483-114.902614.354-73.7782
464.9861.64973.41354.095-0.23485.605-0.39640.332-0.0697-0.44130.19070.1407-1.2524-0.291-0.04690.9223-0.0885-0.02921.058-0.04830.5371-125.005832.2306-66.4719
475.86981.22521.88654.75941.90247.58490.4499-0.2002-0.2349-0.3311-0.0110.36390.0510.4397-0.35640.3628-0.03290.03270.2672-0.06060.5741-117.616825.3743-56.2503
483.8545-1.22230.55654.91392.13668.9215-0.1806-0.43970.14270.29950.034-0.3064-0.3138-0.56790.16030.3298-0.0108-0.13980.6227-0.12520.3646-114.071829.8824-40.1834
491.2214-0.77212.36915.18251.78466.88820.18240.0692-0.647-0.25280.3745-1.39960.12571.7166-0.69550.5257-0.1701-0.08551.3649-0.19341.0618-97.661727.8049-30.803
501.86890.97762.74440.66962.22227.88291.0333-0.6952-0.29441.3569-0.1496-0.9750.89290.9249-0.98561.2089-0.0811-0.4661.1098-0.01991.1684-93.347429.3386-2.9963
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 34 )A7 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 66 )A35 - 66
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 154 )A67 - 154
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 174 )A155 - 174
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 234 )A175 - 234
6X-RAY DIFFRACTION6chain 'A' and (resid 235 through 332 )A235 - 332
7X-RAY DIFFRACTION7chain 'A' and (resid 333 through 367 )A333 - 367
8X-RAY DIFFRACTION8chain 'B' and (resid 6 through 90 )B6 - 90
9X-RAY DIFFRACTION9chain 'B' and (resid 91 through 154 )B91 - 154
10X-RAY DIFFRACTION10chain 'B' and (resid 155 through 274 )B155 - 274
11X-RAY DIFFRACTION11chain 'B' and (resid 275 through 367 )B275 - 367
12X-RAY DIFFRACTION12chain 'C' and (resid 6 through 116 )C6 - 116
13X-RAY DIFFRACTION13chain 'C' and (resid 117 through 366 )C117 - 366
14X-RAY DIFFRACTION14chain 'D' and (resid 7 through 34 )D7 - 34
15X-RAY DIFFRACTION15chain 'D' and (resid 35 through 66 )D35 - 66
16X-RAY DIFFRACTION16chain 'D' and (resid 67 through 116 )D67 - 116
17X-RAY DIFFRACTION17chain 'D' and (resid 117 through 154 )D117 - 154
18X-RAY DIFFRACTION18chain 'D' and (resid 155 through 194 )D155 - 194
19X-RAY DIFFRACTION19chain 'D' and (resid 195 through 234 )D195 - 234
20X-RAY DIFFRACTION20chain 'D' and (resid 235 through 274 )D235 - 274
21X-RAY DIFFRACTION21chain 'D' and (resid 275 through 294 )D275 - 294
22X-RAY DIFFRACTION22chain 'D' and (resid 295 through 332 )D295 - 332
23X-RAY DIFFRACTION23chain 'D' and (resid 333 through 356 )D333 - 356
24X-RAY DIFFRACTION24chain 'E' and (resid 8 through 42 )E8 - 42
25X-RAY DIFFRACTION25chain 'E' and (resid 43 through 134 )E43 - 134
26X-RAY DIFFRACTION26chain 'E' and (resid 135 through 174 )E135 - 174
27X-RAY DIFFRACTION27chain 'E' and (resid 175 through 254 )E175 - 254
28X-RAY DIFFRACTION28chain 'E' and (resid 255 through 332 )E255 - 332
29X-RAY DIFFRACTION29chain 'E' and (resid 333 through 365 )E333 - 365
30X-RAY DIFFRACTION30chain 'F' and (resid 3 through 116 )F3 - 116
31X-RAY DIFFRACTION31chain 'F' and (resid 117 through 332 )F117 - 332
32X-RAY DIFFRACTION32chain 'F' and (resid 333 through 368 )F333 - 368
33X-RAY DIFFRACTION33chain 'G' and (resid 6 through 42 )G6 - 42
34X-RAY DIFFRACTION34chain 'G' and (resid 43 through 76 )G43 - 76
35X-RAY DIFFRACTION35chain 'G' and (resid 77 through 116 )G77 - 116
36X-RAY DIFFRACTION36chain 'G' and (resid 117 through 194 )G117 - 194
37X-RAY DIFFRACTION37chain 'G' and (resid 195 through 254 )G195 - 254
38X-RAY DIFFRACTION38chain 'G' and (resid 255 through 368 )G255 - 368
39X-RAY DIFFRACTION39chain 'H' and (resid 8 through 154 )H8 - 154
40X-RAY DIFFRACTION40chain 'H' and (resid 155 through 369 )H155 - 369
41X-RAY DIFFRACTION41chain 'I' and (resid 6 through 48 )I6 - 48
42X-RAY DIFFRACTION42chain 'I' and (resid 49 through 86 )I49 - 86
43X-RAY DIFFRACTION43chain 'I' and (resid 87 through 116 )I87 - 116
44X-RAY DIFFRACTION44chain 'I' and (resid 117 through 154 )I117 - 154
45X-RAY DIFFRACTION45chain 'I' and (resid 155 through 174 )I155 - 174
46X-RAY DIFFRACTION46chain 'I' and (resid 175 through 194 )I175 - 194
47X-RAY DIFFRACTION47chain 'I' and (resid 195 through 234 )I195 - 234
48X-RAY DIFFRACTION48chain 'I' and (resid 235 through 294 )I235 - 294
49X-RAY DIFFRACTION49chain 'I' and (resid 295 through 332 )I295 - 332
50X-RAY DIFFRACTION50chain 'I' and (resid 333 through 367 )I333 - 367

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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://pdbjlvh1.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