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- PDB-5bp4: Modifying region (DH-ER-KR) of a mycocerosic acid synthase-like (... -

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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: 5bp4
タイトルModifying region (DH-ER-KR) of a mycocerosic acid synthase-like (MAS-like) PKS
要素Mycocerosic acid synthase
キーワードTRANSFERASE / polyketide / dehydratase / ketoreductase / enoylreductase
機能・相同性
機能・相同性情報


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / 転移酵素; アシル基を移すもの; アミノアシル基以外のアシル基を移すもの / fatty acid biosynthetic process / oxidoreductase activity / plasma membrane / cytoplasm
類似検索 - 分子機能
: / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. ...: / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
類似検索 - ドメイン・相同性
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Mycocerosic acid synthase-like polyketide synthase
類似検索 - 構成要素
生物種Mycobacterium smegmatis (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.75 Å
データ登録者Herbst, D.A. / Jakob, P.R. / Zaehringer, F. / Maier, T.
資金援助 スイス, 4件
組織認可番号
Swiss National Science Foundation125357 スイス
Swiss National Science Foundation138262 スイス
Swiss National Science Foundation159696 スイス
Swiss National Science Foundation145023 スイス
引用ジャーナル: Nature / : 2016
タイトル: Mycocerosic acid synthase exemplifies the architecture of reducing polyketide synthases.
著者: Herbst, D.A. / Jakob, R.P. / Zahringer, F. / Maier, T.
履歴
登録2015年5月27日登録サイト: RCSB / 処理サイト: PDBE
改定 1.02016年3月9日Provider: repository / タイプ: Initial release
改定 1.12016年3月30日Group: Database references
改定 1.22016年4月6日Group: Database references
改定 1.32016年12月28日Group: Structure summary
改定 1.42017年9月6日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.52024年1月10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: Mycocerosic acid synthase
B: Mycocerosic acid synthase
C: Mycocerosic acid synthase
D: Mycocerosic acid synthase
E: Mycocerosic acid synthase
F: Mycocerosic acid synthase
G: Mycocerosic acid synthase
H: Mycocerosic acid synthase
I: Mycocerosic acid synthase
J: Mycocerosic acid synthase
K: Mycocerosic acid synthase
L: Mycocerosic acid synthase
M: Mycocerosic acid synthase
N: Mycocerosic acid synthase
O: Mycocerosic acid synthase
P: Mycocerosic acid synthase
Q: Mycocerosic acid synthase
R: Mycocerosic acid synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,199,54048
ポリマ-2,177,23818
非ポリマー22,30230
00
1
A: Mycocerosic acid synthase
B: Mycocerosic acid synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)244,8896
ポリマ-241,9152
非ポリマー2,9744
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area9690 Å2
ΔGint-40 kcal/mol
Surface area84970 Å2
手法PISA
2
C: Mycocerosic acid synthase
D: Mycocerosic acid synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)244,8896
ポリマ-241,9152
非ポリマー2,9744
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area9450 Å2
ΔGint-40 kcal/mol
Surface area85370 Å2
手法PISA
3
E: Mycocerosic acid synthase
F: Mycocerosic acid synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)244,1465
ポリマ-241,9152
非ポリマー2,2303
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-37 kcal/mol
Surface area83250 Å2
手法PISA
4
G: Mycocerosic acid synthase
H: Mycocerosic acid synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)244,8896
ポリマ-241,9152
非ポリマー2,9744
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area9190 Å2
ΔGint-38 kcal/mol
Surface area83360 Å2
手法PISA
5
I: Mycocerosic acid synthase
J: Mycocerosic acid synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)244,1465
ポリマ-241,9152
非ポリマー2,2303
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-40 kcal/mol
Surface area67360 Å2
手法PISA
6
K: Mycocerosic acid synthase
L: Mycocerosic acid synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)244,1465
ポリマ-241,9152
非ポリマー2,2303
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-33 kcal/mol
Surface area77450 Å2
手法PISA
7
M: Mycocerosic acid synthase
N: Mycocerosic acid synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)244,8896
ポリマ-241,9152
非ポリマー2,9744
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-36 kcal/mol
Surface area82660 Å2
手法PISA
8
O: Mycocerosic acid synthase
P: Mycocerosic acid synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)244,1465
ポリマ-241,9152
非ポリマー2,2303
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-37 kcal/mol
Surface area65360 Å2
手法PISA
9
Q: Mycocerosic acid synthase
R: Mycocerosic acid synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)243,4024
ポリマ-241,9152
非ポリマー1,4872
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-41 kcal/mol
Surface area48510 Å2
手法PISA
単位格子
Length a, b, c (Å)151.380, 190.370, 270.840
Angle α, β, γ (deg.)95.58, 91.92, 103.65
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
Mycocerosic acid synthase


分子量: 120957.656 Da / 分子数: 18 / 由来タイプ: 組換発現
由来: (組換発現) Mycobacterium smegmatis (バクテリア)
: ATCC 700084 / mc(2)155 / 細胞株: Mybobacterium / 遺伝子: MSMEG_4727 / プラスミド: pNIC28-Bsa4
発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)
参照: UniProt: A0R1E8, mycocerosate synthase
#2: 化合物...
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


分子量: 743.405 Da / 分子数: 30 / 由来タイプ: 合成 / : C21H28N7O17P3

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実験情報

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実験

実験手法: X線回折

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試料調製

結晶マシュー密度: 3.04 Å3/Da / 溶媒含有率: 59.51 %
結晶化温度: 277.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7
詳細: Crystallization condition: 0.052 M MgCl2, 0.052 M CaCl2, 5.88% (w/v) PEG 3350, 20 % (v/v) ethylene glycol, 0.05 M MES pH 7.0 Protein/buffer: 20.3 mg/ml protein, 1.5 mM NADP+, 0.02 mM HEPES pH ...詳細: Crystallization condition: 0.052 M MgCl2, 0.052 M CaCl2, 5.88% (w/v) PEG 3350, 20 % (v/v) ethylene glycol, 0.05 M MES pH 7.0 Protein/buffer: 20.3 mg/ml protein, 1.5 mM NADP+, 0.02 mM HEPES pH 7.4, 0.25 M NaCl, 5 % (v/v) Glycerol, 0.005 M DTT. Seeding

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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: SLS / ビームライン: X06SA / 波長: 0.97626 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2013年12月19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: 0.97626 Å / 相対比: 1
反射解像度: 3.75→78.62 Å / Num. obs: 296164 / % possible obs: 99.9 % / 冗長度: 9 % / Biso Wilson estimate: 132.22 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.25 / Net I/σ(I): 8.95
反射 シェル解像度: 3.75→3.85 Å / 冗長度: 9.26 % / Rmerge(I) obs: 3.159 / Num. unique all: 21835 / CC1/2: 0.449 / % possible all: 98.9

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解析

ソフトウェア
名称バージョン分類
BUSTER2.10.2精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 2FR0, 5bp2, 2vz9
解像度: 3.75→78.62 Å / Cor.coef. Fo:Fc: 0.8883 / Cor.coef. Fo:Fc free: 0.9075 / 交差検証法: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.573
Rfactor反射数%反射Selection details
Rfree0.2401 2985 1.01 %thin shell
Rwork0.2298 ---
obs0.2299 296153 98.96 %-
原子変位パラメータBiso mean: 171.34 Å2
Baniso -1Baniso -2Baniso -3
1-7.536 Å223.653 Å2-9.3253 Å2
2---12.9181 Å20.4492 Å2
3---5.3821 Å2
Refine analyzeLuzzati coordinate error obs: 0.538 Å
精密化ステップサイクル: LAST / 解像度: 3.75→78.62 Å
タンパク質核酸リガンド溶媒全体
原子数131922 0 1192 0 133114
拘束条件
Refine-IDタイプDev idealRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.008265384HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.97479085HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d75094SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes3029HARMONIC2
X-RAY DIFFRACTIONt_gen_planes41120HARMONIC5
X-RAY DIFFRACTIONt_it265384HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion2.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion17799SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact293670SEMIHARMONIC4
LS精密化 シェル解像度: 3.75→3.85 Å
Rfactor反射数%反射
Rfree0.2645 199 1 %
Rwork0.253 21621 -
obs--98.84 %
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)
12.68841.3548-1.67495.2498-2.65354.8454-0.03550.36020.6185-0.58250.40080.0026-0.0743-0.0188-0.3653-0.1296-0.0602-0.0911-0.17550.1078-0.1145-28.1-4.13830.2974
21.94050.8266-0.9750.2575-0.12361.1613-0.02450.3666-0.0379-0.36930.03160.3078-0.2991-0.4564-0.00710.4504-0.0004-0.01020.4241-0.1969-0.4247-17.0801-33.9869-56.3906
32.4786-0.1465-1.31752.38630.21894.0049-0.15560.3301-0.4778-0.25690.111-0.30970.44990.03980.0446-0.06150.03690.025-0.1756-0.186-0.0631-10.0341-46.193510.5059
44.14692.9971-0.27642.91441.04723.15570.06820.1450.5346-0.57650.1468-0.4129-0.99710.2279-0.21510.6181-0.38760.38680.1285-0.2879-0.62131.9057-23.7112-36.8915
55.75312.2936-1.62822.7412-1.04873.4997-0.0176-0.10360.12060.26520.20370.40580.1513-0.2201-0.1861-0.17860.1039-0.0631-0.14320.1596-0.0629-59.5673-26.813130.2541
63.6831-0.6938-1.80926.08060.96055.59870.03250.19170.4650.3474-0.13270.5047-0.9417-0.27310.10020.31470.30350.2559-0.38970.0663-0.0739-63.32640.944182.7356
72.30510.4593-0.22881.9037-0.5634.22930.0505-0.33960.0950.15920.011-0.03740.04850.0584-0.0615-0.2010.0716-0.0849-0.0234-0.0879-0.1064-14.3028-24.77443.3257
81.75550.6655-1.48255.2056-1.86964.34290.26020.1967-0.3155-0.4295-0.1620.4110.1912-0.5316-0.0982-0.10520.0942-0.04350.1569-0.1611-0.2054-56.31-26.937679.2224
94.00591.8978-1.36567.4606-4.93196.7353-0.02150.0239-0.3246-0.51250.1464-0.52920.60730.5602-0.1249-0.28210.0943-0.0765-0.5237-0.26130.1231-44.836247.3389.7223
104.51542.02160.6661.45051.13496.0405-0.02380.5814-0.4161-0.2335-0.0390.5422-0.1553-0.4470.0628-0.01290.1767-0.0119-0.1431-0.16440.1888-36.461114.478439.1676
112.80510.2746-0.9772.93850.73734.0293-0.04880.2642-0.2774-0.50110.1503-0.4691-0.01220.055-0.1015-0.111-0.02160.0536-0.3253-0.01150.0227-26.56785.6487105.9006
128.05211.3661-1.27643.87550.492.84510.1159-0.27920.55830.19120.01030.2525-0.50840.1056-0.12620.34220.04090.3462-0.506-0.1653-0.091-16.314625.88556.5769
1312.80155.6402-5.2964.8321-3.18786.0323-0.0454-0.81750.23140.3821-0.15660.0140.47070.54970.2020.07920.1636-0.2555-0.7698-0.0068-0.1102-73.946123.8129121.0148
141.7552-2.9351-1.44044.293-1.1359-0.37280.02810.02380.47640.1305-0.17660.2235-0.38-0.13130.14850.39170.0436-0.12480.0483-0.2995-0.2008-82.71755.7734171.673
152.35711.46550.40934.1271.13163.77090.386-0.40330.12320.5462-0.3528-0.0860.043-0.2931-0.0332-0.0763-0.0864-0.0874-0.28560.0559-0.1793-30.508228.4689138.0123
161.78910.653-1.26484.3749-1.32935.987-0.0954-0.1763-0.1067-0.0494-0.11380.14260.0384-0.37360.20910.0383-0.16510.07170.0591-0.1947-0.3182-74.333328.0532170.2525
176.92643.4699-3.44234.2431-1.09074.93860.4328-0.70570.98160.1168-0.03060.7518-0.13790.322-0.4022-0.0554-0.06250.0143-0.2911-0.1824-0.1163-94.630778.2873205.9675
18-1.30692.87940.47282.4281-0.6501-0.0817-0.04160.15410.11470.09260.01470.2677-0.3948-0.35450.02690.22970.2520.02740.01380.0447-0.0899-106.9711107.406264.5275
193.14981.1799-0.68242.97531.40276.51780.3765-0.56260.21650.6938-0.3893-0.05270.07770.29010.0128-0.0301-0.5884-0.02660.6184-0.2815-0.7884-53.197785.8184229.5835
201.1055-0.0189-0.62174.0235-2.1596.2984-0.03720.0808-0.2530.01930.04820.25460.1529-0.1313-0.01090.0581-0.21670.1561-0.0665-0.3939-0.192-96.740480.6502260.3796
214.22272.3316-2.20196.0386-3.70266.24180.3052-0.14540.5447-0.80980.2388-0.3152-0.07170.5607-0.544-0.0021-0.09850.5047-0.4292-0.31650.0584-64.0557100.9625176.0598
227.14641.97270.77631.5942-0.19125.3982-0.22830.39010.1451-0.30890.20870.47-0.0948-0.38140.0196-0.02980.0558-0.1494-0.0668-0.15090.0338-52.397766.8683130.606
233.43020.2164-0.75942.45461.10882.87730.366-0.2913-0.36290.3249-0.3824-0.53220.45590.07960.0165-0.2357-0.1578-0.0950.3157-0.0728-0.3872-47.270162.7165198.4029
246.87251.3043-2.15543.01260.32743.2218-0.0566-0.74750.913-0.2844-0.1250.1966-0.2404-0.10260.18160.14720.312-0.0275-0.2154-0.2284-0.1301-32.486879.4194148.0926
254.54971.5740.07775.0172.83597.1918-0.58120.0276-0.0815-0.34960.23370.06680.1704-0.09860.34750.1725-0.12430.2336-0.4258-0.1378-0.4055-107.96164.412177.4049
264.82861.1509-2.51760.34770.02916.55030.01090.09180.2399-0.5429-0.07-0.51720.0803-0.1620.05920.13850.1187-0.0193-0.04480.4281-0.0545-125.561436.5918130.7115
273.0673-1.10471.92432.4191-1.44983.43050.02130.30290.1262-0.10180.06510.6997-0.110.0789-0.0863-0.16380.0293-0.28510.0167-0.076-0.0962-124.66442.9612199.4833
285.27441.0110.05063.9086-1.2333.27640.12170.1737-0.4166-0.2268-0.33280.30790.239-0.21830.211-0.0112-0.0174-0.35920.12220.1156-0.323-143.088125.9662151.1663
296.61522.57291.35942.76670.51984.4379-0.0243-0.4212-0.23690.289-0.2711-0.308-0.09510.27970.29540.14790.0232-0.0524-0.0263-0.0706-0.475-77.429727.7465206.9417
305.7977-0.98421.18546.2724-0.55882.0445-0.10630.2385-0.206-0.3087-0.0831-0.11510.3606-0.06250.1894-0.2105-0.0413-0.0920.19280.4846-0.2296-70.9742-14.398254.9318
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116-0.58561.31550.92950.86670.49270.1507-0.0036-0.0152-0.00870.01670.02980.0239-0.00560.0366-0.02610.026-0.11710.20750.0080.00090.0159-96.5409-60.3359173.9135
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|896 - A|1176 }
2X-RAY DIFFRACTION2{ A|1192 - A|1400 }
3X-RAY DIFFRACTION3{ A|1419 - A|1746 }
4X-RAY DIFFRACTION4{ A|1761 - A|2008 }
5X-RAY DIFFRACTION5{ B|896 - B|1176 }
6X-RAY DIFFRACTION6{ B|1192 - B|1400 }
7X-RAY DIFFRACTION7{ B|1419 - B|1746 }
8X-RAY DIFFRACTION8{ B|1761 - B|2008 }
9X-RAY DIFFRACTION9{ C|896 - C|1176 }
10X-RAY DIFFRACTION10{ C|1192 - C|1400 }
11X-RAY DIFFRACTION11{ C|1419 - C|1746 }
12X-RAY DIFFRACTION12{ C|1761 - C|2008 }
13X-RAY DIFFRACTION13{ D|896 - D|1176 }
14X-RAY DIFFRACTION14{ D|1192 - D|1400 }
15X-RAY DIFFRACTION15{ D|1419 - D|1746 }
16X-RAY DIFFRACTION16{ D|1761 - D|2008 }
17X-RAY DIFFRACTION17{ E|896 - E|1176 }
18X-RAY DIFFRACTION18{ E|1192 - E|1400 }
19X-RAY DIFFRACTION19{ E|1419 - E|1746 }
20X-RAY DIFFRACTION20{ E|1761 - E|2008 }
21X-RAY DIFFRACTION21{ F|896 - F|1176 }
22X-RAY DIFFRACTION22{ F|1192 - F|1400 }
23X-RAY DIFFRACTION23{ F|1419 - F|1746 }
24X-RAY DIFFRACTION24{ F|1761 - F|2008 }
25X-RAY DIFFRACTION25{ G|896 - G|1176 }
26X-RAY DIFFRACTION26{ G|1192 - G|1400 }
27X-RAY DIFFRACTION27{ G|1419 - G|1746 }
28X-RAY DIFFRACTION28{ G|1761 - G|2008 }
29X-RAY DIFFRACTION29{ H|896 - H|1176 }
30X-RAY DIFFRACTION30{ H|1192 - H|1400 }
31X-RAY DIFFRACTION31{ H|1419 - H|1746 }
32X-RAY DIFFRACTION32{ H|1761 - H|2008 }
33X-RAY DIFFRACTION33{ I|896 - I|1176 }
34X-RAY DIFFRACTION34{ I|1419 - I|1746 }
35X-RAY DIFFRACTION35{ J|896 - J|1176 }
36X-RAY DIFFRACTION36{ J|1192 - J|1400 }
37X-RAY DIFFRACTION37{ J|1419 - J|1746 }
38X-RAY DIFFRACTION38{ J|1761 - J|2008 }
39X-RAY DIFFRACTION39{ K|896 - K|1176 }
40X-RAY DIFFRACTION40{ K|1192 - K|1400 }
41X-RAY DIFFRACTION41{ K|1419 - K|1746 }
42X-RAY DIFFRACTION42{ K|1761 - K|2008 }
43X-RAY DIFFRACTION43{ L|896 - L|1176 }
44X-RAY DIFFRACTION44{ L|1419 - L|1746 }
45X-RAY DIFFRACTION45{ L|1761 - L|2008 }
46X-RAY DIFFRACTION46{ M|896 - M|1176 }
47X-RAY DIFFRACTION47{ M|1192 - M|1400 }
48X-RAY DIFFRACTION48{ M|1419 - M|1746 }
49X-RAY DIFFRACTION49{ M|1761 - M|2008 }
50X-RAY DIFFRACTION50{ N|896 - N|1176 }
51X-RAY DIFFRACTION51{ N|1192 - N|1400 }
52X-RAY DIFFRACTION52{ N|1419 - N|1746 }
53X-RAY DIFFRACTION53{ N|1761 - N|2008 }
54X-RAY DIFFRACTION54{ O|896 - O|1178 }
55X-RAY DIFFRACTION55{ O|1419 - O|1746 }
56X-RAY DIFFRACTION56{ P|896 - P|1176 }
57X-RAY DIFFRACTION57{ P|1192 - P|1400 }
58X-RAY DIFFRACTION58{ P|1419 - P|1746 }
59X-RAY DIFFRACTION59{ P|1761 - P|2008 }
60X-RAY DIFFRACTION60{ Q|896 - Q|1176 }
61X-RAY DIFFRACTION61{ Q|1419 - Q|1745 }
62X-RAY DIFFRACTION62{ R|897 - R|1176 }
63X-RAY DIFFRACTION63{ R|1419 - R|1746 }
64X-RAY DIFFRACTION64{ A|883 - A|895 }
65X-RAY DIFFRACTION65{ A|1177 - A|1191 }
66X-RAY DIFFRACTION66{ A|1401 - A|1418 }
67X-RAY DIFFRACTION67{ A|1747 - A|1760 }
68X-RAY DIFFRACTION68{ B|883 - B|895 }
69X-RAY DIFFRACTION69{ B|1177 - B|1191 }
70X-RAY DIFFRACTION70{ B|1401 - B|1418 }
71X-RAY DIFFRACTION71{ B|1747 - B|1760 }
72X-RAY DIFFRACTION72{ C|883 - C|895 }
73X-RAY DIFFRACTION73{ C|1177 - C|1191 }
74X-RAY DIFFRACTION74{ C|1401 - C|1418 }
75X-RAY DIFFRACTION75{ C|1747 - C|1760 }
76X-RAY DIFFRACTION76{ D|883 - D|895 }
77X-RAY DIFFRACTION77{ D|1177 - D|1191 }
78X-RAY DIFFRACTION78{ D|1401 - D|1418 }
79X-RAY DIFFRACTION79{ D|1747 - D|1760 }
80X-RAY DIFFRACTION80{ E|1177 - E|1191 }
81X-RAY DIFFRACTION81{ E|1401 - E|1418 }
82X-RAY DIFFRACTION82{ E|1747 - E|1760 }
83X-RAY DIFFRACTION83{ F|1177 - F|1191 }
84X-RAY DIFFRACTION84{ F|1401 - F|1418 }
85X-RAY DIFFRACTION85{ F|1747 - F|1760 }
86X-RAY DIFFRACTION86{ G|1177 - G|1191 }
87X-RAY DIFFRACTION87{ G|1401 - G|1418 }
88X-RAY DIFFRACTION88{ G|1747 - G|1760 }
89X-RAY DIFFRACTION89{ H|1177 - H|1191 }
90X-RAY DIFFRACTION90{ H|1401 - H|1418 }
91X-RAY DIFFRACTION91{ H|1747 - H|1760 }
92X-RAY DIFFRACTION92{ I|1177 - I|1191 }
93X-RAY DIFFRACTION93{ I|1401 - I|1418 }
94X-RAY DIFFRACTION94{ I|1747 - I|1759 }
95X-RAY DIFFRACTION95{ J|1177 - J|1191 }
96X-RAY DIFFRACTION96{ J|1401 - J|1418 }
97X-RAY DIFFRACTION97{ J|1747 - J|1760 }
98X-RAY DIFFRACTION98{ K|1177 - K|1191 }
99X-RAY DIFFRACTION99{ K|1401 - K|1418 }
100X-RAY DIFFRACTION100{ K|1747 - K|1760 }
101X-RAY DIFFRACTION101{ L|1177 - L|1196 }
102X-RAY DIFFRACTION102{ L|1402 - L|1418 }
103X-RAY DIFFRACTION103{ L|1747 - L|1760 }
104X-RAY DIFFRACTION104{ M|1177 - M|1191 }
105X-RAY DIFFRACTION105{ M|1401 - M|1418 }
106X-RAY DIFFRACTION106{ M|1747 - M|1760 }
107X-RAY DIFFRACTION107{ N|1177 - N|1191 }
108X-RAY DIFFRACTION108{ N|1401 - N|1418 }
109X-RAY DIFFRACTION109{ N|1747 - N|1760 }
110X-RAY DIFFRACTION110{ O|1407 - O|1418 }
111X-RAY DIFFRACTION111{ O|1747 - O|1756 }
112X-RAY DIFFRACTION112{ P|1177 - P|1191 }
113X-RAY DIFFRACTION113{ P|1401 - P|1418 }
114X-RAY DIFFRACTION114{ P|1747 - P|1760 }
115X-RAY DIFFRACTION115{ R|1177 - R|1191 }
116X-RAY DIFFRACTION116{ R|1747 - R|1759 }

+
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