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- PDB-5wab: Crystal Structure of Bifidobacterium adolescentis GH3 beta-glucosidase -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 5wab
タイトルCrystal Structure of Bifidobacterium adolescentis GH3 beta-glucosidase
要素Putative beta-glucosidase
キーワードHYDROLASE / GH3 / beta-glucosidase / Bifidobacterium / adolescentis
機能・相同性
機能・相同性情報


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
類似検索 - 分子機能
: / : / Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily ...: / : / Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
生物種Bifidobacterium adolescentis (バクテリア)
手法X線回折 / 分子置換 / 解像度: 2.45 Å
データ登録者Florindo, R.N. / Nascimento, A.S. / Polikarpov, I.
引用ジャーナル: Biochimie / : 2018
タイトル: Structural and biochemical characterization of a GH3 beta-glucosidase from the probiotic bacteria Bifidobacterium adolescentis.
著者: Florindo, R.N. / Souza, V.P. / Manzine, L.R. / Camilo, C.M. / Marana, S.R. / Polikarpov, I. / Nascimento, A.S.
履歴
登録2017年6月26日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年4月4日Provider: repository / タイプ: Initial release
改定 1.12018年4月25日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
改定 1.22023年10月4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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Putative beta-glucosidase
B: Putative beta-glucosidase
C: Putative beta-glucosidase
D: Putative beta-glucosidase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)324,8715
ポリマ-324,7794
非ポリマー921
25,2571402
1
A: Putative beta-glucosidase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)81,2872
ポリマ-81,1951
非ポリマー921
181
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
2
B: Putative beta-glucosidase


分子量 (理論値)分子数
合計 (水以外)81,1951
ポリマ-81,1951
非ポリマー00
181
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
3
C: Putative beta-glucosidase


分子量 (理論値)分子数
合計 (水以外)81,1951
ポリマ-81,1951
非ポリマー00
181
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
4
D: Putative beta-glucosidase


分子量 (理論値)分子数
合計 (水以外)81,1951
ポリマ-81,1951
非ポリマー00
181
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)94.610, 96.430, 106.770
Angle α, β, γ (deg.)87.76, 89.11, 61.00
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
Putative beta-glucosidase


分子量: 81194.719 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a) (バクテリア)
: ATCC 15703 / DSM 20083 / NCTC 11814 / E194a / 遺伝子: BAD_1194 / プラスミド: pETTRXA-1a/LIC
発現宿主: Escherichia coli str. K-12 substr. DH10B (大腸菌)
参照: UniProt: A1A2P2
#2: 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: 1 / 由来タイプ: 合成 / : C3H8O3
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1402 / 由来タイプ: 天然 / : H2O

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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: 2.62 Å3/Da / 溶媒含有率: 53.04 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8
詳細: 0.1 M HEPES pH 8.5, 0.2 M sodium chloride, 29% PEG 3350, 3% glycerol

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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: 回転陽極 / タイプ: RIGAKU ULTRAX 18 / 波長: 1.5418 Å
検出器タイプ: MAR scanner 345 mm plate / 検出器: IMAGE PLATE / 日付: 2013年12月5日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.5418 Å / 相対比: 1
反射解像度: 2.45→48.4 Å / Num. obs: 103722 / % possible obs: 85.52 % / 冗長度: 4 % / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.118 / Net I/σ(I): 10.5
反射 シェル解像度: 2.45→2.538 Å / 冗長度: 3.6 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8470 / CC1/2: 0.63 / Rpim(I) all: 0.594 / % possible all: 69.65

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.12_2829: ???)精密化
XDSデータ削減
PHASER位相決定
XDSデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 2X40
解像度: 2.45→44.511 Å / SU ML: 0.3 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 23.12 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.234 5227 5.04 %
Rwork0.1949 --
obs0.1969 103704 85.53 %
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
精密化ステップサイクル: LAST / 解像度: 2.45→44.511 Å
タンパク質核酸リガンド溶媒全体
原子数20359 0 6 1402 21767
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00420824
X-RAY DIFFRACTIONf_angle_d0.67428377
X-RAY DIFFRACTIONf_dihedral_angle_d10.22312281
X-RAY DIFFRACTIONf_chiral_restr0.0483166
X-RAY DIFFRACTIONf_plane_restr0.0053740
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.47790.30121540.25262655X-RAY DIFFRACTION68
2.4779-2.5070.31121250.26362658X-RAY DIFFRACTION71
2.507-2.53760.31571380.26612740X-RAY DIFFRACTION70
2.5376-2.56970.31321670.25822772X-RAY DIFFRACTION73
2.5697-2.60350.30111510.24932776X-RAY DIFFRACTION72
2.6035-2.63920.28191630.24332841X-RAY DIFFRACTION75
2.6392-2.67690.26431510.24842913X-RAY DIFFRACTION75
2.6769-2.71680.2871560.24012927X-RAY DIFFRACTION77
2.7168-2.75930.24521600.23322939X-RAY DIFFRACTION76
2.7593-2.80450.28831740.24163041X-RAY DIFFRACTION80
2.8045-2.85280.25281490.22623121X-RAY DIFFRACTION80
2.8528-2.90470.28811590.23333147X-RAY DIFFRACTION83
2.9047-2.96060.27671870.23133228X-RAY DIFFRACTION84
2.9606-3.0210.28791850.23753236X-RAY DIFFRACTION85
3.021-3.08670.26251780.23083355X-RAY DIFFRACTION88
3.0867-3.15840.2761860.21663428X-RAY DIFFRACTION89
3.1584-3.23740.2621780.20233479X-RAY DIFFRACTION90
3.2374-3.32490.22651830.19953512X-RAY DIFFRACTION92
3.3249-3.42270.23091780.18723530X-RAY DIFFRACTION92
3.4227-3.53310.22681660.18583585X-RAY DIFFRACTION93
3.5331-3.65940.19641940.17823640X-RAY DIFFRACTION94
3.6594-3.80580.20241930.16723611X-RAY DIFFRACTION94
3.8058-3.97890.22511650.16493661X-RAY DIFFRACTION95
3.9789-4.18850.18121770.16353662X-RAY DIFFRACTION95
4.1885-4.45070.19981900.15783685X-RAY DIFFRACTION95
4.4507-4.7940.19021890.15193642X-RAY DIFFRACTION96
4.794-5.27580.20192070.1693676X-RAY DIFFRACTION96
5.2758-6.03760.21722040.17893671X-RAY DIFFRACTION96
6.0376-7.60050.21731920.19013694X-RAY DIFFRACTION96
7.6005-44.51840.21632280.18713652X-RAY DIFFRACTION96
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.1134-0.4664-0.37992.37430.50161.89850.0711-0.3527-0.0520.3195-0.0609-0.15760.00060.2366-0.07540.318-0.0382-0.03040.3112-0.00460.2439-8.5287-48.062727.4303
22.3953-0.9551-0.68891.54761.46872.17120.1802-0.29880.2202-0.0776-0.0523-0.3474-0.26430.2818-0.08050.2115-0.05750.01360.2499-0.00460.2874-11.3864-29.627932.9132
30.4007-0.0991-0.67140.32630.46730.71130.0391-0.0242-0.06290.06180.0472-0.0204-0.03780.1131-0.05040.2310.0534-0.0550.16140.01260.2341-25.3332-34.142238.1397
41.50650.6013-0.92340.344-0.17860.62170.1455-0.0565-0.1570.0275-0.0834-0.0977-0.1111-0.0214-0.07350.24170.0305-0.0430.18690.02750.1752-27.4092-39.918834.0383
51.95780.8231-0.77571.80120.39131.3815-0.04680.0544-0.2226-0.0666-0.0378-0.0974-0.0066-0.17430.08360.18530.0489-0.01640.16010.01450.1399-29.2803-43.441926.843
61.14530.5660.05221.37090.41791.60760.0597-0.2457-0.14670.3060.0331-0.27210.33120.0693-0.05750.20880.0146-0.04780.20950.05120.2482-21.1527-58.189927.93
71.9861.9536-0.26255.6961-1.46531.8637-0.08140.4486-0.034-0.60120.2562-0.09390.32920.0791-0.17820.26210.0384-0.02120.26910.00060.194-25.0608-59.246416.0042
80.8013-0.00990.06931.5081.46482.17430.174-0.16530.0761-0.03430.2054-0.6109-0.34510.3381-0.32720.2985-0.08140.07330.2545-0.05540.2944-7.0339-31.785428.1533
91.93670.27470.88554.24040.7463.27790.3241-0.48170.34710.3372-0.2258-0.1949-0.30480.1467-0.19610.3574-0.05010.02010.3006-0.0690.2827-17.3969-8.954854.236
101.5651-0.91010.08190.75240.41773.67810.2179-0.17330.1677-0.16520.2703-0.18640.11430.5937-0.29290.2658-0.0489-0.06170.3788-0.01110.4174-7.1787-28.414651.4168
111.86260.4689-1.38531.9509-0.8631.9611-0.0216-0.07570.3519-0.02450.0894-0.9982-0.09580.377-0.12270.4237-0.13310.06640.4551-0.05310.5205-1.8128-17.429853.2498
123.47650.98121.00480.3741-0.3192.00340.2366-0.74630.08790.4656-0.2405-0.185-0.30240.0803-0.03590.4589-0.1334-0.05240.4204-0.00730.2673-15.4769-25.753463.5064
131.0678-0.1347-0.14852.53631.42172.05660.122-0.17110.03220.421-0.1243-0.43810.0741-0.3523-0.02380.2483-0.01210.01790.292-0.06210.2893-21.3845-23.1254.0884
140.3091-0.10070.04870.55890.2140.63450.0908-0.22340.0850.1522-0.0208-0.1062-0.20990.0915-0.03530.2458-0.0057-0.0150.2225-0.00930.2052-30.7891-26.985946.9914
152.82931.09891.3721.14290.73233.38820.35340.36230.51950.05790.171-0.2897-0.62250.0704-0.36830.47540.08930.05370.30710.00070.5326-35.4124-7.967530.0423
160.2751-0.1164-0.52090.15270.17021.08810.0649-0.09180.10050.36190.1515-0.2154-0.31380.00290.01740.43250.0691-0.06310.31810.15060.2613-39.6233-15.037422.4548
171.93441.0839-0.0641.5487-0.17971.59190.2534-0.03610.36790.0262-0.1338-0.0129-0.41-0.0257-0.1450.35980.09190.04270.17170.00420.2899-32.4678-15.219435.074
188.16936.68624.39957.24551.90273.9092-0.41990.33990.7118-0.50611.03440.1259-0.84250.3003-0.25340.3596-0.05860.10530.3009-0.13380.5215-27.5903-7.826528.1024
191.2586-0.28790.6951.6338-0.46031.30070.0896-0.01150.1349-0.3297-0.01450.1613-0.0719-0.081-0.06730.24190.06430.04280.20290.01250.1765-43.7937-23.411229.5966
203.02631.1298-1.10360.8459-0.47670.3684-0.29510.2885-0.5990.0150.23460.1570.2385-0.73690.03260.7122-0.01810.04250.5651-0.00030.3678-59.0132-33.866322.3791
212.2583-1.8244-0.42051.8278-0.83123.61070.19270.01780.0257-0.4660.4846-0.6069-0.58250.2025-0.5860.2951-0.04370.01280.298-0.06250.560360.029428.6815-8.0811
221.57280.1197-0.28151.33480.65920.5859-0.05460.16840.0379-0.18110.1909-0.2761-0.12730.1646-0.1290.23840.00310.0650.22730.01430.26753.87649.2911-15.0825
230.35640.5096-0.26131.30030.10831.07720.0303-0.0456-0.0113-0.05650.0014-0.11330.08230.0586-0.01610.14870.04290.02620.14150.01710.18844.5311.7266-1.9243
241.1631-0.0749-0.71431.55470.10361.88210.00090.13360.18850.08170.0632-0.0469-0.2254-0.1524-0.04310.22740.0290.02550.21720.02490.29947.755529.8323-0.1757
250.357-0.8084-0.93082.47020.71733.20020.2942-0.49690.320.52860.5005-0.8684-0.33730.6965-0.30940.1661-0.0218-0.0030.25560.00680.384154.246628.55617.85
262.18081.10290.96252.90842.31752.3259-0.45060.3262-0.1012-0.3530.5623-0.2577-0.19410.6546-0.14210.2621-0.03220.07320.3232-0.04950.459567.682711.4046-16.5879
273.09061.5326-0.67772.1686-1.73081.5701-0.37130.21030.1205-0.11110.4957-0.24690.071-0.09470.03940.29190.07780.14890.3626-0.05120.343448.231-8.455-23.4832
282.9486-0.54960.53473.0712-0.50934.8732-0.54330.559-0.3531-0.5362-0.26360.2480.59150.55260.7360.43230.02420.04040.4884-0.10360.449150.0535-16.1132-35.7446
293.7522-0.06180.7731.1751-1.18781.28460.11040.58410.46210.1114-0.0203-0.14740.08840.3663-0.11910.4584-0.02690.15490.31990.00040.279747.86572.8061-36.6607
302.68650.65723.02363.8732-1.24864.5004-0.19710.46030.308-1.1173-0.6074-0.346-0.36750.76090.48680.72830.17380.12040.24060.06070.424652.559114.8432-25.4122
313.28940.27291.05670.9630.28641.4211-0.25950.82280.4041-0.21410.0449-0.3682-0.02340.31670.24470.6838-0.03170.23130.38330.0540.42350.60082.5954-38.8865
321.9455-1.464-0.50591.3120.67492.93390.08240.3551-0.0237-0.7266-0.1072-0.0549-0.36640.14270.07990.5143-0.01250.04930.37080.00410.270638.75041.7953-36.075
331.5721-0.0119-1.0971.87211.4031.81950.3780.56910.1172-0.9171-0.287-0.1499-0.3465-0.2278-0.08930.50210.13030.05740.3657-0.10060.327935.8928-6.7545-39.8015
341.35910.2175-0.41190.3291-0.41940.41530.04030.41090.0235-0.18270.0714-0.20390.11330.1822-0.11740.34410.01740.0590.2818-0.09460.314846.2861-4.7014-28.0109
350.9622-0.6516-0.13640.74080.16390.560.0321-0.1196-0.2009-0.2520.03370.0744-0.12920.0028-0.03920.2750.018-0.00850.20060.00490.216830.32883.8764-12.3415
361.1275-0.9759-0.27290.82390.10632.3260.08460.0970.0315-0.14250.04990.30790.3869-0.2324-0.20360.2266-0.05260.01240.15470.00880.341632.624-6.7445-9.4546
370.8225-0.8880.20951.1341-0.70791.9872-0.02850.0941-0.1593-0.1494-0.057-0.12650.33660.29140.0760.26860.01940.00560.18530.00830.326751.3875-18.9389-7.066
38-0.0248-0.0326-0.47841.40580.41991.5305-0.4607-0.008-0.4217-0.00610.2529-0.11330.43270.1430.1220.2350.07070.02370.2231-0.00220.32147.3738-12.6438-4.7724
390.371-0.62610.15361.45720.72122.37760.2259-0.2418-0.22420.2252-0.2134-0.87440.57270.4672-0.10820.15010.0253-0.02690.29240.12240.437846.0716-7.16327.4023
401.14340.19630.62971.6534-0.24961.356-0.0538-0.2561-0.19250.3774-0.06850.0522-0.0869-0.13560.12140.24140.0356-0.01180.23790.06670.202436.537-7.86319.74
410.2764-0.6775-0.7153.77640.93972.4657-0.242-0.1174-0.1066-0.18180.05490.8936-0.1382-0.10070.14030.3704-0.0481-0.01520.5635-0.14770.5972-84.7803-54.56445.2897
420.12810.3867-0.28531.4818-1.55442.2096-0.0066-0.0452-0.00280.06880.0270.0225-0.0560.02030.01190.31670.87440.83420.5894-0.32260.7279-89.5793-41.117850.9574
431.23170.4522-0.14731.43510.33771.03610.0532-0.05820.0580.1583-0.16150.36520.1031-0.25450.09990.2426-0.01380.01830.2895-0.04940.2087-68.1183-47.736155.2758
441.8541-0.24020.34041.9439-0.20461.90440.13270.12530.03890.1903-0.20350.33140.0535-0.0232-0.00730.2303-0.04710.01450.2692-0.0160.2719-65.5747-57.018742.1464
450.6288-0.818-1.16051.87691.1662.87750.15940.6762-0.2362-0.0954-0.46960.4304-0.2888-0.6520.24530.3142-0.010.060.4648-0.19290.4683-75.8351-61.022831.3072
461.21470.64560.14690.6257-0.31390.3241-0.0715-0.0806-0.05510.4512-0.33640.70290.3885-0.64160.39180.3404-0.07360.1570.4172-0.06550.4641-80.7086-56.876753.829
473.5123-1.55910.8412.1802-1.3190.80730.1497-0.07210.51920.5054-0.4678-0.12470.2017-0.72980.10020.44720.04570.12470.3585-0.09280.2411-64.2729-25.198473.7728
481.0132-0.4419-0.25911.8631-1.30071.01640.1580.0140.4566-0.0138-0.06410.6572-0.1628-0.44120.09880.34980.03870.09370.5561-0.20330.4822-80.1266-25.827563.8608
492.37040.4279-0.34180.9930.1213.5104-0.30140.2601-0.20540.0829-0.69360.5203-0.6271-0.61320.33450.43280.16360.09430.4469-0.18990.5535-78.7827-16.175260.382
501.3599-1.1089-0.84792.37840.75481.80650.17190.01880.2331-0.2069-0.27590.4929-0.338-0.27470.11960.3622-0.0095-0.02580.4612-0.120.3579-71.2233-18.208257.9182
515.1029-1.14340.76980.2552-0.344.64760.4201-0.1910.2193-0.18680.17370.6285-0.411-0.0145-0.4080.3390.18470.02750.2911-0.03390.2806-67.1115-15.116955.4605
522.12660.8780.33022.506-0.39490.1709-0.2991-0.6640.5218-0.2043-0.43830.49670.1592-0.46390.54660.47840.04380.02480.4879-0.13170.302-67.0178-11.988467.7528
531.26410.6633-0.26161.3868-1.00730.78010.36470.35220.15090.1754-0.45680.2177-0.3413-0.02150.05210.260.06890.0580.2906-0.15410.3225-64.3399-24.042263.2798
540.79140.3263-0.26071.01030.42110.36160.1019-0.10020.17780.1247-0.0030.0304-0.1421-0.1812-0.05290.27150.07210.02930.3476-0.0390.1978-60.9217-34.159757.0596
551.78420.7605-0.09362.2109-0.18555.9488-0.49740.02230.2725-0.11580.28070.40420.6174-0.31020.45460.35720.01220.00880.2426-0.00190.2538-50.2177-41.672857.9599
561.7961-0.1938-0.29471.40280.62570.26140.0431-0.05840.29810.465-0.0033-0.0660.0730.05530.03020.2918-0.0411-0.04560.27330.02160.1733-53.5596-36.001370.275
571.0069-0.5204-0.01060.83940.09781.38070.1168-0.2942-0.11290.2975-0.16650.2149-0.0599-0.09620.02380.468-0.08730.0360.336-0.00590.1833-55.3774-47.383974.9288
582.2057-0.96510.84672.51391.9656.558-0.3707-0.1252-0.17770.7036-0.3701-0.23170.83540.78030.68380.3488-0.0566-0.00350.30630.10920.2387-50.931-57.427666.2099
590.2782-0.0777-0.78361.52221.22723.83260.1399-0.067-0.06370.03620.0865-0.15450.68360.7002-0.11960.35520.0818-0.04730.1720.07110.2945-43.286-57.39358.2059
601.3812-0.10160.16081.85020.08040.66640.1437-0.09740.08250.0787-0.0867-0.57210.19720.3679-0.02840.37090.0064-0.04940.34410.10810.2384-43.2324-52.694566.0753
611.60670.72660.91950.7686-0.0941.08590.0535-0.1099-0.21050.1266-0.08130.10320.30380.0615-0.04540.26780.00680.05120.19150.02960.207-8.80336.190823.7158
620.881-0.3024-1.30871.16640.90612.3531-0.0868-0.0043-0.20630.1365-0.1199-0.04510.0987-0.25440.160.2073-0.0498-0.0390.29-0.02840.2701-11.4784-1.83767.3855
630.8902-0.6597-0.07560.5689-0.07270.2930.0299-0.0631-0.1188-0.0913-0.0410.10.1038-0.0657-0.00970.19470.0393-0.01910.18130.03810.15983.92115.89874.5476
641.58770.2175-0.15210.70930.99661.30310.1105-0.0821-0.06390.1382-0.04160.04350.10650.0431-0.05250.2160.0212-0.01970.1444-0.00180.20296.457514.824414.0228
651.51180.34820.06430.05480.02490.52250.0521-0.02210.28560.18320.30130.0011-0.35740.0611-0.27520.24590.04280.03810.2192-0.03690.25434.401614.515521.2348
661.06460.56410.15052.02321.4891.28050.1909-0.0339-0.17091.0337-0.0714-0.41270.1784-0.1715-0.07390.36740.0386-0.04050.27220.02660.15956.145218.051931.0301
671.22-0.75030.00181.87911.66072.57020.0396-0.13130.07760.0933-0.34180.49290.0067-0.51970.25920.18540.03450.00570.2668-0.00540.2276-14.52727.678215.6066
682.7177-0.3375-0.99022.5592-1.41411.3005-0.45230.01190.0975-0.046-0.21590.08810.0699-0.47370.47650.365-0.0297-0.12010.3591-0.0740.1857-10.6845-9.0597-5.428
690.7058-0.5627-0.12411.9288-1.24551.12070.09910.2827-0.2086-0.42010.32010.52450.0435-0.031-0.15430.4577-0.0671-0.07210.3677-0.07150.2224-5.9177-23.5299-12.3206
704.2883-0.9765-0.9814.42571.01312.8473-0.54510.15960.21260.4990.6019-0.33440.30330.60190.15410.294-0.0175-0.02780.22080.0060.35894.6822-31.9792.8713
711.81830.58690.04653.1213-0.09151.01470.0673-0.0798-0.40710.09130.023-0.06940.5667-0.187-0.0180.3697-0.02640.02610.21180.01250.30444.4614-24.1018-1.3265
721.51010.23720.07143.17270.07111.7506-0.07290.0787-0.3393-0.2626-0.0971-0.02780.1927-0.07070.11210.2557-0.03670.03770.2094-0.00660.24264.5859-24.0623-9.7814
733.71420.6169-2.64020.9845-0.12554.31230.36540.22211.01930.0220.59610.1608-0.12420.0677-0.68390.2641-0.06170.02630.1818-0.03330.2712-4.6533-13.7883-2.5507
741.60610.69380.36020.95230.71670.6278-0.1533-0.2125-0.1512-0.28590.0642-0.048-0.0887-0.18320.04740.2306-0.01230.00970.19830.03440.17757.3183-7.5502-4.4315
754.34780.93891.94541.4507-1.81974.8351-0.1405-0.32250.7076-0.2605-0.0284-0.57620.1641-0.3509-0.02050.28660.0452-0.01320.1292-0.02920.211916.53355.6242-6.4061
760.5059-0.05370.5611.8801-0.34890.32320.01180.19220.0839-0.26590.00480.21350.0919-0.092-0.01820.38840.028-0.02780.37470.00550.1144-0.980.8622-19.3336
770.97190.9814-0.54142.05220.2991.143-0.23080.36690.033-0.28850.0490.2539-0.0399-0.36590.14180.28840.0578-0.08050.37440.0220.181-1.2938.1478-16.4064
784.65450.44083.11893.2385-0.20095.3602-0.03220.59070.06950.2053-0.001-0.36930.14530.6169-0.06270.26090.0768-0.03880.19270.0030.2813.112221.8383-6.7541
791.82361.96640.03542.94030.76740.5689-0.16050.2690.2572-0.60.27550.117-0.181-0.1106-0.04370.373-0.0036-0.0050.21930.07690.26265.751813.3556-21.0072
800.69170.0454-0.59480.85860.01670.38080.03180.11580.13780.08120.0155-0.0982-0.15230.07560.03520.38710.046-0.11330.23830.09490.216414.249521.4879-17.5516
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 22:52 )A22 - 52
2X-RAY DIFFRACTION2( CHAIN A AND RESID 65:102 )A65 - 102
3X-RAY DIFFRACTION3( CHAIN A AND RESID 103:134 )A103 - 134
4X-RAY DIFFRACTION4( CHAIN A AND RESID 135:179 )A135 - 179
5X-RAY DIFFRACTION5( CHAIN A AND RESID 180:230 )A180 - 230
6X-RAY DIFFRACTION6( CHAIN A AND RESID 231:263 )A231 - 263
7X-RAY DIFFRACTION7( CHAIN A AND RESID 264:280 )A264 - 280
8X-RAY DIFFRACTION8( CHAIN A AND RESID 281:317 )A281 - 317
9X-RAY DIFFRACTION9( CHAIN A AND RESID 318:332 )A318 - 332
10X-RAY DIFFRACTION10( CHAIN A AND RESID 333:359 )A333 - 359
11X-RAY DIFFRACTION11( CHAIN A AND RESID 360:374 )A360 - 374
12X-RAY DIFFRACTION12( CHAIN A AND RESID 375:445 )A375 - 445
13X-RAY DIFFRACTION13( CHAIN A AND RESID 446:473 )A446 - 473
14X-RAY DIFFRACTION14( CHAIN A AND RESID 474:548 )A474 - 548
15X-RAY DIFFRACTION15( CHAIN A AND RESID 549:562 )A549 - 562
16X-RAY DIFFRACTION16( CHAIN A AND RESID 563:570 )A563 - 570
17X-RAY DIFFRACTION17( CHAIN A AND RESID 571:611 )A571 - 611
18X-RAY DIFFRACTION18( CHAIN A AND RESID 612:621 )A612 - 621
19X-RAY DIFFRACTION19( CHAIN A AND RESID 622:662 )A622 - 662
20X-RAY DIFFRACTION20( CHAIN A AND RESID 663:681 )A663 - 681
21X-RAY DIFFRACTION21( CHAIN B AND RESID 23:45 )B23 - 45
22X-RAY DIFFRACTION22( CHAIN B AND RESID 46:124 )B46 - 124
23X-RAY DIFFRACTION23( CHAIN B AND RESID 125:224 )B125 - 224
24X-RAY DIFFRACTION24( CHAIN B AND RESID 225:265 )B225 - 265
25X-RAY DIFFRACTION25( CHAIN B AND RESID 266:286 )B266 - 286
26X-RAY DIFFRACTION26( CHAIN B AND RESID 287:312 )B287 - 312
27X-RAY DIFFRACTION27( CHAIN B AND RESID 313:321 )B313 - 321
28X-RAY DIFFRACTION28( CHAIN B AND RESID 322:333 )B322 - 333
29X-RAY DIFFRACTION29( CHAIN B AND RESID 334:346 )B334 - 346
30X-RAY DIFFRACTION30( CHAIN B AND RESID 347:356 )B347 - 356
31X-RAY DIFFRACTION31( CHAIN B AND RESID 357:385 )B357 - 385
32X-RAY DIFFRACTION32( CHAIN B AND RESID 386:427 )B386 - 427
33X-RAY DIFFRACTION33( CHAIN B AND RESID 428:444 )B428 - 444
34X-RAY DIFFRACTION34( CHAIN B AND RESID 445:490 )B445 - 490
35X-RAY DIFFRACTION35( CHAIN B AND RESID 491:522 )B491 - 522
36X-RAY DIFFRACTION36( CHAIN B AND RESID 523:543 )B523 - 543
37X-RAY DIFFRACTION37( CHAIN B AND RESID 544:579 )B544 - 579
38X-RAY DIFFRACTION38( CHAIN B AND RESID 580:620 )B580 - 620
39X-RAY DIFFRACTION39( CHAIN B AND RESID 621:628 )B621 - 628
40X-RAY DIFFRACTION40( CHAIN B AND RESID 629:677 )B629 - 677
41X-RAY DIFFRACTION41( CHAIN C AND RESID 23:52 )C23 - 52
42X-RAY DIFFRACTION42( CHAIN C AND RESID 65:66 )C65 - 66
43X-RAY DIFFRACTION43( CHAIN C AND RESID 67:192 )C67 - 192
44X-RAY DIFFRACTION44( CHAIN C AND RESID 193:246 )C193 - 246
45X-RAY DIFFRACTION45( CHAIN C AND RESID 247:266 )C247 - 266
46X-RAY DIFFRACTION46( CHAIN C AND RESID 267:315 )C267 - 315
47X-RAY DIFFRACTION47( CHAIN C AND RESID 316:325 )C316 - 325
48X-RAY DIFFRACTION48( CHAIN C AND RESID 326:364 )C326 - 364
49X-RAY DIFFRACTION49( CHAIN C AND RESID 368:386 )C368 - 386
50X-RAY DIFFRACTION50( CHAIN C AND RESID 387:426 )C387 - 426
51X-RAY DIFFRACTION51( CHAIN C AND RESID 427:432 )C427 - 432
52X-RAY DIFFRACTION52( CHAIN C AND RESID 433:446 )C433 - 446
53X-RAY DIFFRACTION53( CHAIN C AND RESID 447:469 )C447 - 469
54X-RAY DIFFRACTION54( CHAIN C AND RESID 473:524 )C473 - 524
55X-RAY DIFFRACTION55( CHAIN C AND RESID 525:529 )C525 - 529
56X-RAY DIFFRACTION56( CHAIN C AND RESID 530:557 )C530 - 557
57X-RAY DIFFRACTION57( CHAIN C AND RESID 558:620 )C558 - 620
58X-RAY DIFFRACTION58( CHAIN C AND RESID 621:628 )C621 - 628
59X-RAY DIFFRACTION59( CHAIN C AND RESID 629:645 )C629 - 645
60X-RAY DIFFRACTION60( CHAIN C AND RESID 646:674 )C646 - 674
61X-RAY DIFFRACTION61( CHAIN D AND RESID 25:47 )D25 - 47
62X-RAY DIFFRACTION62( CHAIN D AND RESID 48:108 )D48 - 108
63X-RAY DIFFRACTION63( CHAIN D AND RESID 109:203 )D109 - 203
64X-RAY DIFFRACTION64( CHAIN D AND RESID 204:240 )D204 - 240
65X-RAY DIFFRACTION65( CHAIN D AND RESID 241:251 )D241 - 251
66X-RAY DIFFRACTION66( CHAIN D AND RESID 252:271 )D252 - 271
67X-RAY DIFFRACTION67( CHAIN D AND RESID 272:309 )D272 - 309
68X-RAY DIFFRACTION68( CHAIN D AND RESID 310:316 )D310 - 316
69X-RAY DIFFRACTION69( CHAIN D AND RESID 317:340 )D317 - 340
70X-RAY DIFFRACTION70( CHAIN D AND RESID 374:390 )D374 - 390
71X-RAY DIFFRACTION71( CHAIN D AND RESID 391:430 )D391 - 430
72X-RAY DIFFRACTION72( CHAIN D AND RESID 431:465 )D431 - 465
73X-RAY DIFFRACTION73( CHAIN D AND RESID 466:476 )D466 - 476
74X-RAY DIFFRACTION74( CHAIN D AND RESID 477:520 )D477 - 520
75X-RAY DIFFRACTION75( CHAIN D AND RESID 521:526 )D521 - 526
76X-RAY DIFFRACTION76( CHAIN D AND RESID 527:582 )D527 - 582
77X-RAY DIFFRACTION77( CHAIN D AND RESID 583:628 )D583 - 628
78X-RAY DIFFRACTION78( CHAIN D AND RESID 629:638 )D629 - 638
79X-RAY DIFFRACTION79( CHAIN D AND RESID 639:650 )D639 - 650
80X-RAY DIFFRACTION80( CHAIN D AND RESID 651:682 )D651 - 682

+
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

-
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

+
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

+
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