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- PDB-4cql: Crystal structure of heterotetrameric human ketoacyl reductase co... -

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基本情報

登録情報
データベース: PDB / ID: 4cql
タイトルCrystal structure of heterotetrameric human ketoacyl reductase complexed with NAD
要素
  • CARBONYL REDUCTASE FAMILY MEMBER 4
  • ESTRADIOL 17-BETA-DEHYDROGENASE 8
キーワードOXIDOREDUCTASE (酸化還元酵素) / KAR / 3-KETOACYL-ACP REDUCTASE / HSD8 / 17-BETA HYDROXYSTEROID DEHYDROGENASE / HSD17B8 / 3R- HYDROXYACYL-COA DEHYDROGENASE / CARBOBYL REDUCTASE TYPE4 / NADH (ニコチンアミドアデニンジヌクレオチド) / NADP (ニコチンアミドアデニンジヌクレオチドリン酸) / NADPH (ニコチンアミドアデニンジヌクレオチドリン酸) / HETERO TETRAMER
機能・相同性
機能・相同性情報


NADPHデヒドロゲナーゼ (キノン) / (3R)-hydroxyacyl-CoA dehydrogenase (NAD+) activity / : / estrogen biosynthetic process / NADPH dehydrogenase (quinone) activity / 3α(17β)-ヒドロキシステロイドデヒドロゲナーゼ (NAD+) / oxidoreductase complex / Fatty acyl-CoA biosynthesis / testosterone dehydrogenase (NAD+) activity / NADH binding ...NADPHデヒドロゲナーゼ (キノン) / (3R)-hydroxyacyl-CoA dehydrogenase (NAD+) activity / : / estrogen biosynthetic process / NADPH dehydrogenase (quinone) activity / 3α(17β)-ヒドロキシステロイドデヒドロゲナーゼ (NAD+) / oxidoreductase complex / Fatty acyl-CoA biosynthesis / testosterone dehydrogenase (NAD+) activity / NADH binding / 17beta-estradiol 17-dehydrogenase / NAD(P)H dehydrogenase (quinone) activity / estradiol 17-beta-dehydrogenase [NAD(P)] activity / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / mitochondrial envelope / daunorubicin metabolic process / doxorubicin metabolic process / protein heterotetramerization / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / androgen metabolic process / quinone binding / NADPH binding / fatty acid biosynthetic process / protein homotetramerization / ミトコンドリアマトリックス / 細胞膜
類似検索 - 分子機能
PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / ロスマンフォールド / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-oxoacyl-[acyl-carrier-protein] reductase / (3R)-3-hydroxyacyl-CoA dehydrogenase
類似検索 - 構成要素
生物種HOMO SAPIENS (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.85 Å
データ登録者Venkatesan, R. / Sah-Teli, S.K. / Awoniyi, L.O. / Jiang, G. / Prus, P. / Kastaniotis, A.J. / Hiltunen, J.K. / Wierenga, R.K. / Chen, Z.
引用ジャーナル: Nat.Commun. / 年: 2014
タイトル: Insights Into Mitochondrial Fatty Acid Synthesis from the Structure of Heterotetrameric 3-Ketoacyl-Acp Reductase/3R-Hydroxyacyl-Coa Dehydrogenase.
著者: Venkatesan, R. / Sah-Teli, S.K. / Awoniyi, L.O. / Jiang, G. / Prus, P. / Kastaniotis, A.J. / Hiltunen, J.K. / Wierenga, R.K. / Chen, Z.
履歴
登録2014年2月19日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02014年9月10日Provider: repository / タイプ: Initial release
改定 1.12014年9月17日Group: Database references
改定 1.22023年12月20日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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: ESTRADIOL 17-BETA-DEHYDROGENASE 8
B: CARBONYL REDUCTASE FAMILY MEMBER 4
C: CARBONYL REDUCTASE FAMILY MEMBER 4
D: ESTRADIOL 17-BETA-DEHYDROGENASE 8
E: ESTRADIOL 17-BETA-DEHYDROGENASE 8
F: CARBONYL REDUCTASE FAMILY MEMBER 4
G: CARBONYL REDUCTASE FAMILY MEMBER 4
H: ESTRADIOL 17-BETA-DEHYDROGENASE 8
I: ESTRADIOL 17-BETA-DEHYDROGENASE 8
J: CARBONYL REDUCTASE FAMILY MEMBER 4
K: CARBONYL REDUCTASE FAMILY MEMBER 4
L: ESTRADIOL 17-BETA-DEHYDROGENASE 8
M: ESTRADIOL 17-BETA-DEHYDROGENASE 8
N: CARBONYL REDUCTASE FAMILY MEMBER 4
O: CARBONYL REDUCTASE FAMILY MEMBER 4
P: ESTRADIOL 17-BETA-DEHYDROGENASE 8
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)431,69324
ポリマ－426,38616
非ポリマー5,3078
水3,927218
1
E: ESTRADIOL 17-BETA-DEHYDROGENASE 8
F: CARBONYL REDUCTASE FAMILY MEMBER 4
G: CARBONYL REDUCTASE FAMILY MEMBER 4
H: ESTRADIOL 17-BETA-DEHYDROGENASE 8
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)107,9236
ポリマ－106,5964
非ポリマー1,3272
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area15430 Å2
ΔGint-111.1 kcal/mol
Surface area31730 Å2
手法PISA
2
A: ESTRADIOL 17-BETA-DEHYDROGENASE 8
B: CARBONYL REDUCTASE FAMILY MEMBER 4
C: CARBONYL REDUCTASE FAMILY MEMBER 4
D: ESTRADIOL 17-BETA-DEHYDROGENASE 8
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)107,9236
ポリマ－106,5964
非ポリマー1,3272
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area14950 Å2
ΔGint-108.7 kcal/mol
Surface area31360 Å2
手法PISA
3
M: ESTRADIOL 17-BETA-DEHYDROGENASE 8
N: CARBONYL REDUCTASE FAMILY MEMBER 4
O: CARBONYL REDUCTASE FAMILY MEMBER 4
P: ESTRADIOL 17-BETA-DEHYDROGENASE 8
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)107,9236
ポリマ－106,5964
非ポリマー1,3272
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area15230 Å2
ΔGint-107 kcal/mol
Surface area31980 Å2
手法PISA
4
I: ESTRADIOL 17-BETA-DEHYDROGENASE 8
J: CARBONYL REDUCTASE FAMILY MEMBER 4
K: CARBONYL REDUCTASE FAMILY MEMBER 4
L: ESTRADIOL 17-BETA-DEHYDROGENASE 8
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)107,9236
ポリマ－106,5964
非ポリマー1,3272
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area14790 Å2
ΔGint-103.5 kcal/mol
Surface area31330 Å2
手法PISA
単位格子
Length a, b, c (Å)87.150, 237.110, 87.350
Angle α, β, γ (deg.)90.00, 94.52, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
ESTRADIOL 17-BETA-DEHYDROGENASE 8 / 3-KETOACYL REDUCTASE ALPHA SUBUNIT / 1 7-BETA-HYDROXYSTEROID D 17-BETA-HSD 8 / 3-OXOACYL-[ACYL- ...3-KETOACYL REDUCTASE ALPHA SUBUNIT / 1 7-BETA-HYDROXYSTEROID D 17-BETA-HSD 8 / 3-OXOACYL-[ACYL-CARRIER-PROTEIN] REDUCTASE / PROTEIN KE6 / KE-6 / REALLY INTERESTING NEW GENE 2 PROTEIN / TESTOSTERONE 17-BETA-DEHYDROGENASE 8


分子量: 26999.738 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PLR631 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 / Variant (発現宿主): PLYSS RARE
参照: UniProt: Q92506, 3-oxoacyl-[acyl-carrier-protein] reductase, 17beta-estradiol 17-dehydrogenase, 3α(17β)-ヒドロキシステロイドデヒドロゲナーゼ (NAD+)
#2: タンパク質
CARBONYL REDUCTASE FAMILY MEMBER 4 / 3-KETOACYL REDUCTASE BETA SUBUNIT / QUINONE REDUCTASE CBR4


分子量: 26298.506 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PLR631 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 / Variant (発現宿主): PLYSS RARE
参照: UniProt: Q8N4T8, 3-oxoacyl-[acyl-carrier-protein] reductase
#3: 化合物
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / ニコチンアミドアデニンジヌクレオチド


分子量: 663.425 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C21H27N7O14P2 / コメント: NAD*YM
#4: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 218 / 由来タイプ: 天然 / 式: H2O
配列の詳細N-TERMINAL HIS TAG

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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 Å3/Da / 溶媒含有率: 40 % / 解説: NONE
結晶化pH: 5
詳細: 15% PEG3350, 0.4 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE PH 5.0

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: ESRF / ビームライン: ID29 / 波長: 0.9763
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2010年7月1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: 0.9763 Å / 相対比: 1
Reflection twinOperator: L,-K,H / Fraction: 0.32
反射解像度: 2.85→49.78 Å / Num. obs: 75354 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / 冗長度: 2.9 % / Biso Wilson estimate: 57.7 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.6
反射 シェル解像度: 2.85→3 Å / 冗長度: 3.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1 / % possible all: 95.1

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)精密化
iMOSFLMデータ削減
SCALA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: PDB ENTRY 2PD6

2pd6


解像度: 2.85→49.776 Å / σ(F): 1.34 / 位相誤差: 33.79 / 立体化学のターゲット値: TWIN_LSQ_F
Rfactor反射数%反射
Rfree0.2358 3958 5.3 %
Rwork0.1826 --
obs0.185 75310 91.7 %
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: 2.85→49.776 Å
タンパク質核酸リガンド溶媒全体
原子数26263 0 352 218 26833
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00226925
X-RAY DIFFRACTIONf_angle_d0.48736571
X-RAY DIFFRACTIONf_dihedral_angle_d12.7229215
X-RAY DIFFRACTIONf_chiral_restr0.0194472
X-RAY DIFFRACTIONf_plane_restr0.0024730
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8504-2.89960.30032150.22943749X-RAY DIFFRACTION91
2.8996-2.95230.34161780.22353635X-RAY DIFFRACTION90
2.9523-3.0090.28561760.21373759X-RAY DIFFRACTION90
3.009-3.07040.27421870.22213617X-RAY DIFFRACTION90
3.0704-3.13720.29411970.2133675X-RAY DIFFRACTION90
3.1372-3.21010.25731670.20843699X-RAY DIFFRACTION90
3.2101-3.29030.26771980.19863626X-RAY DIFFRACTION89
3.2903-3.37920.25731690.19973675X-RAY DIFFRACTION89
3.3792-3.47860.26061740.1893663X-RAY DIFFRACTION90
3.4786-3.59080.24871950.17573608X-RAY DIFFRACTION89
3.5908-3.7190.22611910.17623601X-RAY DIFFRACTION89
3.719-3.86780.2131960.16863625X-RAY DIFFRACTION88
3.8678-4.04370.22311870.17273583X-RAY DIFFRACTION87
4.0437-4.25660.21081850.1643550X-RAY DIFFRACTION86
4.2566-4.52290.22761800.14993508X-RAY DIFFRACTION85
4.5229-4.87150.18921700.14853426X-RAY DIFFRACTION83
4.8715-5.36050.20841750.17373316X-RAY DIFFRACTION81
5.3605-6.13340.24251700.2073218X-RAY DIFFRACTION78
6.1334-7.71690.23751570.17873170X-RAY DIFFRACTION77
7.7169-38.13910.21012050.17973889X-RAY DIFFRACTION93
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1887-0.9687-0.87992.72680.59071.84080.17320.20190.1506-0.69930.176-0.3755-0.09180.8308-0.19820.4503-0.21540.04330.8677-0.09920.26553.4659-38.78367.3076
20.52650.0667-0.33630.0272-0.10130.3962-0.03920.1131-0.0174-0.0910.02990.04590.0232-0.0768-0.0290.5517-0.1134-0.31930.7607-0.16670.4776-6.813-40.65094.8554
32.53880.8088-1.31681.12150.00332.8698-0.18450.4924-0.313-0.3384-0.15320.27830.0836-0.0720.0310.5433-0.166-0.06820.6695-0.22010.3745-10.5971-48.69815.1831
40.3467-0.1454-0.33562.84861.75762.93570.10290.4773-0.4357-0.29-0.08970.120.0161-0.23660.20240.2439-0.0928-0.04080.6067-0.18790.2827-11.3306-39.812117.9701
51.9222-0.25840.20341.6586-0.5061.2258-0.27310.13440.0188-0.02360.3348-0.27530.2709-0.26480.0840.2717-0.0976-0.06480.321-0.04060.191-3.7613-39.66823.8404
64.7611-1.93611.32020.8848-0.51261.6018-0.17280.17470.21440.06880.259-0.2063-0.08140.15720.7180.347-0.1351-0.21840.37120.06810.32845.1973-20.88827.3469
71.1792-0.7862-0.26761.9776-0.42340.8904-0.03830.31150.09990.3319-0.2397-0.0586-0.06030.18820.26340.2841-0.0501-0.09190.2785-0.00840.28786.9876-40.765524.1669
80.0482-0.15930.07651.25180.65571.2939-0.2455-0.1741-0.2042-0.13070.0344-0.0356-0.1838-0.0674-0.18260.1264-0.014-0.00550.4213-0.01830.365430.111-41.252328.6003
92.0574-0.0646-0.50223.20731.19691.1106-0.31450.4513-0.2335-0.09160.0017-0.97180.17080.52970.26170.27080.08610.01140.4658-0.02550.63931.1237-47.60531.7703
100.9988-0.60520.47961.52550.00421.2875-0.1165-0.2583-0.16710.3424-0.0067-0.8908-0.17130.05540.0490.3149-0.0161-0.1530.48160.04720.455224.435-41.938144.5096
113.57020.3908-0.46893.6995-0.19722.9043-0.09050.1822-0.36340.1992-0.0967-0.2489-0.07630.14650.13620.15130.0164-0.03160.29280.01240.210311.6358-44.747335.0617
122.3002-0.2696-1.12691.3125-0.64411.4185-0.05280.13760.24170.24830.08620.4628-0.7194-0.3169-0.19010.45120.2058-0.05670.9222-0.02680.377-3.7162-37.147168.2499
130.07050.1161-0.07390.38970.1590.48170.12790.0573-0.13410.21780.0709-0.18580.07640.11080.18750.7135-0.0311-0.21911.1358-0.10880.381510.483-37.533770.578
141.97860.55461.41411.4234-1.09075.53970.2326-0.0681-0.1054-0.3066-0.505-0.1631-0.36070.73930.06741.10340.1764-0.12270.93460.11350.34159.1895-47.728872.7453
151.1134-0.45630.58131.2295-0.07883.2863-0.249-0.5290.04160.32680.0457-0.1611-0.53790.03730.08190.46370.1754-0.15880.78750.02560.266611.3009-39.362658.7873
160.0861-0.0712-0.10750.45-0.19120.328-0.1076-0.2816-0.11850.03240.0143-0.0965-0.13620.0220.28670.49610.117-0.01470.59620.12970.19372.5345-43.237955.9758
172.2276-0.1655-0.25540.90670.44591.4719-0.1874-0.67230.14570.16270.1821-0.09490.0140.1509-0.0120.2530.0378-0.09210.48280.01680.1905-2.079-35.544451.7132
181.7111-1.11071.01651.03780.10012.42420.05940.1077-0.2510.4364-0.01630.3743-0.1335-0.15930.14660.4076-0.04390.13970.72490.1290.2562-30.791-41.315248.7563
190.6201-0.5034-0.44661.10850.67440.9048-0.0792-0.4979-0.13030.5825-0.07370.0491-0.0491-0.23240.21850.4786-0.11890.00190.72990.15130.266-34.6408-39.564640.559
200.0761-0.0068-0.02040.12790.20860.3388-0.11310.02820.08520.0285-0.0938-0.0436-0.3332-0.04250.06530.34980.0159-0.11880.79490.07790.2369-35.0861-30.232137.6326
211.44020.81180.28740.96320.10291.84190.04810.4565-0.18650.2789-0.2126-0.0821-0.0337-0.13480.05780.307-0.1433-0.00850.4849-0.08160.2187-21.9825-44.853733.38
220.9584-0.8771-0.83551.01130.63451.562-0.19620.2818-0.038-0.2884-0.01890.3424-0.0325-0.11750.11960.3168-0.1343-0.05080.3873-0.02450.1899-22.8633-37.334230.2907
231.2113-0.3458-0.44921.41810.90522.4152-0.2783-0.10880.02610.16460.3045-0.11060.30380.1939-0.01830.25970.004-0.0770.34390.00210.1375-14.9684-38.5636.5797
241.78470.85910.80344.53670.47130.39450.3111-0.2638-0.55650.1777-0.15310.05390.1245-0.0524-0.04430.3314-0.0249-0.06570.39020.12070.4093-16.1851-48.296145.192
250.4529-0.10260.17551.4750.15240.09320.1663-0.3188-0.15270.05870.1363-0.10840.096-0.198-0.16160.49070.01630.05420.5391-0.0360.2411-10.5719-38.662348.1228
263.17660.3189-0.15925.43491.7833.37240.0368-0.64570.38420.2295-0.3427-0.7135-0.43890.6329-0.14380.4053-0.0647-0.05840.38220.04850.249749.7357-13.903932.0416
272.22550.5863-0.82353.5494-1.58541.37690.0536-1.3926-0.24970.6191-0.2582-0.0335-0.16460.09510.37670.2760.04650.01010.6985-0.04920.311642.3216-18.585438.8555
281.27560.72650.53791.76570.85741.80550.1216-0.19610.27040.2136-0.10490.1141-0.07480.1146-0.00240.4334-0.1390.02860.6388-0.10730.177234.5013-13.872230.5938
292.1066-0.34110.42872.16620.61851.43210.1923-0.05020.38180.1878-0.3219-0.07220.0565-0.35140.13590.2453-0.09450.03230.3220.02580.208434.6349-11.93619.7835
301.14430.437-0.24683.1016-0.19831.4559-0.0502-0.10390.0001-0.0257-0.0081-0.01540.15350.30670.07910.08420.00860.02280.3792-0.07070.318547.3722-19.187817.7244
312.7045-0.0939-0.65891.15860.57683.03890.19020.1560.34550.16590.0194-0.30550.18160.0117-0.07130.480.0201-0.15120.19660.02580.453373.2879-13.964614.074
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332.4410.79361.25042.4421-0.01652.6228-0.35050.4494-0.0830.1281-0.0446-0.6150.1635-0.11270.36010.35140.01270.05050.55150.17040.640578.4706-10.97213.6665
341.8689-0.1022-0.00470.792-0.21191.3084-0.04150.23490.5114-0.0345-0.075-0.266-0.29110.14370.1010.3686-0.03420.04710.39610.12010.337759.5783-9.90561.4304
350.8094-0.63060.88753.1656-1.37133.0256-0.1047-0.1770.2378-0.2015-0.0342-0.12970.17120.21220.31120.1723-0.00340.05250.5172-0.0260.311554.3484-9.215212.5413
361.8774-0.0265-0.2820.8062-0.24661.67910.21760.1576-0.03650.0596-0.08790.09410.1328-0.15630.03470.86850.10370.0831.1920.07380.273743.9359-18.0737-27.9869
370.79220.8325-0.58110.9935-0.53630.47190.00050.43830.3849-0.87620.1612-0.0958-0.27560.58090.0190.91580.08780.13330.9660.2230.385748.9397-5.9959-28.6021
380.20940.0917-0.13360.4030.3460.53680.03210.32260.1967-0.5741-0.1039-0.1792-0.06290.0003-0.23260.4296-0.04990.07750.80210.21560.250652.3083-13.2903-12.1302
390.36110.07080.16250.37180.24841.59090.09250.37870.0136-0.25720.00360.05560.2328-0.1290.03350.37370.01660.0020.84030.0440.153938.1676-20.6322-9.7413
400.2790.3811-0.09020.80260.32552.4369-0.01160.05230.1023-0.2934-0.05370.3626-0.1557-0.6288-0.55980.35650.1417-0.06740.82420.35330.482411.6264-12.7193-4.9323
411.35720.47041.30590.62760.61442.1810.23290.19290.26150.0412-0.18670.1181-0.0009-0.52970.11850.2451-0.03580.06370.5222-0.08250.229417.9695-15.56689.1598
421.4231-0.49340.2740.91780.09621.54450.03430.35330.3846-0.2844-0.28850.0698-0.24150.04920.22090.2821-0.0879-0.04690.63710.12160.294129.1012-11.2624-0.5641
430.6291-0.01730.81961.072-1.15242.2609-0.17770.32530.17610.3354-0.0250.4893-0.4517-0.4440.23940.30670.17510.03110.55190.00360.374410.0419-74.47592.0385
443.9605-0.39181.34241.2159-0.23081.3184-0.1717-0.7694-0.0750.19840.11450.1862-0.1605-0.3390.0260.2740.1183-0.12190.8557-0.03340.42745.9496-73.5184-3.985
450.8989-0.1660.04550.81790.03321.3196-0.00170.1136-0.04230.1705-0.00640.099-0.1629-0.31780.04170.27380.1101-0.02750.35760.03520.290523.9694-74.8675-4.3997
466.81921.8909-4.48051.4906-0.73753.4454-0.280.23850.3831-0.43950.28-0.0008-0.04130.03020.19610.3698-0.0433-0.09920.20960.02260.153228.9558-72.626329.3754
471.2179-0.06050.25220.76080.16344.26180.4637-0.33750.72150.8069-0.31230.3406-0.2815-0.41260.02950.61350.05160.05290.4440.00310.276930.5333-65.182229.2716
481.50720.90571.84510.91430.76222.58180.5245-0.2883-0.02120.8682-0.16410.07470.18070.0775-0.25610.81990.1588-0.030.5472-0.07320.339236.8301-73.196333.0981
494.8295-0.8704-2.51820.16830.46621.32910.09020.06140.79170.01310.1305-0.5261-0.52220.52780.07990.5959-0.1004-0.06150.75840.08070.773452.5602-57.962917.2344
502.96060.24360.52450.19210.33463.03760.1587-0.12570.29610.1607-0.063-0.0744-0.28480.1245-0.07140.3240.0446-0.07370.2275-0.04040.309238.7039-69.306114.5501
511.48010.11560.4720.6817-0.23290.57370.07010.2218-0.4078-0.06280.0413-0.2260.03760.16170.21020.1727-0.0337-0.09370.8656-0.08420.662971.4513-78.3482.0229
521.18910.0389-0.27810.2383-0.09440.0956-0.09480.1237-0.0842-0.01360.0473-0.1967-0.01720.0463-0.04020.35-0.1434-0.21991.0274-0.05120.965673.9042-76.17089.5175
533.23651.3671-1.37620.5739-0.59151.23750.2342-0.44780.3110.13750.3035-0.3045-0.44740.78460.23240.4615-0.1007-0.01040.6181-0.27650.841765.7955-73.258212.043
540.86530.2406-0.81931.57810.37542.54520.1351-0.1402-0.10430.15710.0268-0.268-0.17660.49-0.1180.26620.0466-0.10280.4563-0.0630.358355.7226-74.84853.4082
554.0146-0.08870.40844.0796-0.17232.35570.15390.38620.0947-0.62930.019-0.3415-0.00320.108-0.01910.399-0.00210.02020.4018-0.03220.236550.232-75.8988-30.4213
560.85730.3557-0.01090.62010.9361.87440.07580.1242-0.0418-0.05940.03830.0895-0.3205-0.0279-0.15790.34920.0323-0.05630.27310.03540.270737.9677-74.228-17.5088
571.3435-3.34560.87599.0068-1.69980.91430.14270.74540.4541-1.4490.14880.37310.05-0.087-0.330.4467-0.09190.0280.8775-0.09970.720545.6222-55.0505-18.4365
580.3982-0.2303-0.38143.8594-0.42560.48220.1440.13680.08790.3940.4322-0.0617-0.17360.0064-0.3280.34690.0228-0.02920.3848-0.03610.373451.9264-67.8394-11.1695
591.1721-1.015-0.08741.96990.81520.5725-0.1427-0.36130.12860.7130.1105-0.2040.06080.26890.00660.3035-0.0615-0.05810.49380.08930.184830.4629-99.534650.5494
601.48020.8081-0.22591.0085-0.19961.0056-0.21160.4015-0.03750.1550.0355-0.4536-0.0450.1249-0.00560.17610.0814-0.14650.522-0.04910.420237.6126-100.018839.1552
611.20230.6426-0.0960.83440.37822.0573-0.19910.1030.20970.1089-0.2448-0.2538-0.4290.28790.40110.2685-0.0283-0.02760.3112-0.0320.193522.6648-93.927433.117
621.6126-0.34660.43991.5813-0.35772.1409-0.08110.2593-0.04370.1313-0.1556-0.11720.1580.00170.17290.10130.03470.0170.3097-0.02280.193919.8575-101.415933.8881
631.4333-0.4492-0.04961.2298-0.04490.4661-0.06310.28780.1706-0.0908-0.1189-0.011-0.1018-0.0252-0.07910.11740.0854-0.07070.48220.08840.278219.913-96.88741.8589
642.8805-0.55570.02993.06951.04821.1466-0.1415-0.03510.24150.37350.20860.1301-0.16630.00420.03170.1792-0.00720.06120.31850.03420.264115.312-92.95248.9243
656.6231.40982.12610.89490.90232.4899-0.04340.0161-0.17920.4129-0.2607-0.23260.212-0.01480.35160.46210.04890.09010.30360.02040.397610.4977-104.268370.9111
660.77620.59650.29032.02180.66371.4858-0.05690.01640.03690.3705-0.2180.53130.4039-0.3367-0.07820.5253-0.13960.12750.3801-0.01150.28734.2069-107.196476.4994
674.1697-1.2174-3.91135.4374-1.66525.2194-0.0851-0.38930.45570.2066-0.11810.5366-0.3638-0.29260.07080.30070.13690.04650.72750.09590.5938-4.1879-96.635475.7751
682.2848-0.1452-0.72980.7368-1.03951.8521-0.1769-0.1965-0.13820.28-0.03630.33660.155-0.17030.23730.3614-0.04210.14280.5705-0.09260.3039-5.2875-102.77962.4161
691.4770.2633-0.1322.4148-0.24951.9131-0.02980.083-0.11080.05360.01670.0686-0.1494-0.2705-0.02290.1845-0.0148-0.01250.2837-0.05470.3185.5405-104.259853.2107
700.1821-0.0644-0.16660.10870.01540.17450.07310.2080.3867-0.05020.11610.02350.01350.01140.56570.21630.0228-0.01841.0976-0.02750.7747-27.0488-99.171136.1633
710.4133-0.0097-0.13920.2383-0.15070.14590.05990.21990.2614-0.031-0.04430.2111-0.0084-0.1247-0.01040.2523-0.00030.03141.2153-0.10321.0032-32.4278-97.990343.3308
727.45610.26850.2771.7-0.32291.25110.06810.0209-0.01370.0424-0.01640.27790.0029-0.23380.00710.3552-0.14710.15181.1685-0.1910.8081-31.1656-110.316847.4479
730.62310.72171.00721.35170.98821.68670.21360.11410.04140.0679-0.20450.26660.3275-0.8030.0310.50160.1904-0.15481.1762-0.19810.5565-18.5212-97.404547.46
741.73480.5052-0.5250.7094-0.40880.71170.0937-0.09490.07210.0555-0.02620.5521-0.0268-0.09360.04630.11880.0032-0.01710.7189-0.08060.6465-17.3205-104.471947.6406
751.29080.3938-0.23840.19360.03531.8122-0.35080.1363-0.24490.0134-0.02460.18420.1293-0.27560.08940.13890.0544-0.01560.5206-0.01350.541-9.8444-104.020743.9554
766.25151.1309-4.73383.6991-2.26744.15370.02920.09661.06660.4867-0.13360.5512-0.46190.15070.06450.34010.189-0.08470.6233-0.12320.5288-9.3363-81.46337.1792
771.2532-0.091-0.31841.12640.28160.5822-0.21840.2757-0.0542-0.1839-0.180.3958-0.2083-0.4679-1.05840.18110.0815-0.13160.5329-0.06440.4977-10.0869-97.798233.0383
780.40780.8026-0.32861.6025-0.52750.88250.01530.43620.0585-0.28270.02590.3935-0.2109-0.36420.1470.42210.0405-0.22390.6423-0.06730.3255-8.1738-97.609312.8254
791.40930.00240.78430.5874-0.5681.3658-0.03080.1979-0.0377-0.22580.09970.3030.0567-0.37510.21450.3102-0.0784-0.22760.6549-0.11590.6166-7.3514-104.201913.6875
803.69390.59080.3250.2811-0.14260.2314-0.13750.7079-0.2926-0.4584-0.04020.27270.1311-0.4057-0.00470.47490.0601-0.13570.75490.01660.4563-0.0119-103.51215.0265
811.420.1609-0.84282.531-0.271.55-0.10760.47420.2009-0.285-0.10020.21080.4026-0.25240.07370.51080.0383-0.090.7493-0.0870.23332.8026-99.17476.2036
823.5924-2.24710.57762.3067-0.70280.4681-0.0890.64520.542-0.24-0.2198-0.165-0.0437-0.18910.110.3809-0.0502-0.09880.67870.06070.26938.3372-90.27067.033
831.75170.11990.79570.9095-0.37591.33820.0780.4214-0.0652-0.3209-0.09940.15830.0805-0.28310.03630.24260.0502-0.00850.48680.01080.186811.2175-99.894318.962
841.4893-0.0012-0.3761.42330.580.6784-0.01240.164-0.0883-0.2148-0.1670.5209-0.0655-0.07890.11310.16470.09210.00930.3491-0.04220.30835.957-98.656326.7513
850.6304-0.2665-0.04344.498-0.73360.9140.17050.2141-0.2262-0.3705-0.4510.04480.2531-0.3254-0.00280.205-0.0664-0.00780.603-0.05690.5242-0.5142-111.024725.5004
860.46450.676-0.39341.771-0.16241.99960.14410.1753-0.0986-0.14440.21960.17530.0372-0.24690.08410.1870.0129-0.12960.5591-0.02940.5659-6.3672-101.119227.2113
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 5 THROUGH 54 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 55 THROUGH 78 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 79 THROUGH 92 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 93 THROUGH 145 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 146 THROUGH 211 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 212 THROUGH 229 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 230 THROUGH 261 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID -1 THROUGH 12 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 13 THROUGH 59 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 60 THROUGH 124 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 125 THROUGH 237 )
12X-RAY DIFFRACTION12CHAIN C AND (RESID 3 THROUGH 32 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 33 THROUGH 59 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 60 THROUGH 73 )
15X-RAY DIFFRACTION15CHAIN C AND (RESID 74 THROUGH 117 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 118 THROUGH 145 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 146 THROUGH 237 )
18X-RAY DIFFRACTION18CHAIN D AND (RESID 6 THROUGH 56 )
19X-RAY DIFFRACTION19CHAIN D AND (RESID 57 THROUGH 78 )
20X-RAY DIFFRACTION20CHAIN D AND (RESID 79 THROUGH 93 )
21X-RAY DIFFRACTION21CHAIN D AND (RESID 94 THROUGH 116 )
22X-RAY DIFFRACTION22CHAIN D AND (RESID 117 THROUGH 143 )
23X-RAY DIFFRACTION23CHAIN D AND (RESID 144 THROUGH 186 )
24X-RAY DIFFRACTION24CHAIN D AND (RESID 187 THROUGH 241 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 242 THROUGH 260 )
26X-RAY DIFFRACTION26CHAIN E AND (RESID 6 THROUGH 34 )
27X-RAY DIFFRACTION27CHAIN E AND (RESID 35 THROUGH 54 )
28X-RAY DIFFRACTION28CHAIN E AND (RESID 55 THROUGH 116 )
29X-RAY DIFFRACTION29CHAIN E AND (RESID 117 THROUGH 186 )
30X-RAY DIFFRACTION30CHAIN E AND (RESID 187 THROUGH 261 )
31X-RAY DIFFRACTION31CHAIN F AND (RESID -4 THROUGH 12 )
32X-RAY DIFFRACTION32CHAIN F AND (RESID 13 THROUGH 35 )
33X-RAY DIFFRACTION33CHAIN F AND (RESID 36 THROUGH 74 )
34X-RAY DIFFRACTION34CHAIN F AND (RESID 75 THROUGH 205 )
35X-RAY DIFFRACTION35CHAIN F AND (RESID 206 THROUGH 237 )
36X-RAY DIFFRACTION36CHAIN G AND (RESID 7 THROUGH 59 )
37X-RAY DIFFRACTION37CHAIN G AND (RESID 60 THROUGH 82 )
38X-RAY DIFFRACTION38CHAIN G AND (RESID 83 THROUGH 169 )
39X-RAY DIFFRACTION39CHAIN G AND (RESID 170 THROUGH 237 )
40X-RAY DIFFRACTION40CHAIN H AND (RESID 4 THROUGH 78 )
41X-RAY DIFFRACTION41CHAIN H AND (RESID 79 THROUGH 144 )
42X-RAY DIFFRACTION42CHAIN H AND (RESID 145 THROUGH 261 )
43X-RAY DIFFRACTION43CHAIN I AND (RESID 4 THROUGH 52 )
44X-RAY DIFFRACTION44CHAIN I AND (RESID 53 THROUGH 78 )
45X-RAY DIFFRACTION45CHAIN I AND (RESID 79 THROUGH 261 )
46X-RAY DIFFRACTION46CHAIN J AND (RESID -1 THROUGH 12 )
47X-RAY DIFFRACTION47CHAIN J AND (RESID 13 THROUGH 42 )
48X-RAY DIFFRACTION48CHAIN J AND (RESID 43 THROUGH 82 )
49X-RAY DIFFRACTION49CHAIN J AND (RESID 83 THROUGH 96 )
50X-RAY DIFFRACTION50CHAIN J AND (RESID 97 THROUGH 237 )
51X-RAY DIFFRACTION51CHAIN K AND (RESID 3 THROUGH 42 )
52X-RAY DIFFRACTION52CHAIN K AND (RESID 43 THROUGH 59 )
53X-RAY DIFFRACTION53CHAIN K AND (RESID 60 THROUGH 96 )
54X-RAY DIFFRACTION54CHAIN K AND (RESID 97 THROUGH 237 )
55X-RAY DIFFRACTION55CHAIN L AND (RESID 5 THROUGH 102 )
56X-RAY DIFFRACTION56CHAIN L AND (RESID 103 THROUGH 199 )
57X-RAY DIFFRACTION57CHAIN L AND (RESID 200 THROUGH 217 )
58X-RAY DIFFRACTION58CHAIN L AND (RESID 218 THROUGH 261 )
59X-RAY DIFFRACTION59CHAIN M AND (RESID 5 THROUGH 34 )
60X-RAY DIFFRACTION60CHAIN M AND (RESID 35 THROUGH 93 )
61X-RAY DIFFRACTION61CHAIN M AND (RESID 94 THROUGH 116 )
62X-RAY DIFFRACTION62CHAIN M AND (RESID 117 THROUGH 186 )
63X-RAY DIFFRACTION63CHAIN M AND (RESID 187 THROUGH 211 )
64X-RAY DIFFRACTION64CHAIN M AND (RESID 212 THROUGH 261 )
65X-RAY DIFFRACTION65CHAIN N AND (RESID -3 THROUGH 35 )
66X-RAY DIFFRACTION66CHAIN N AND (RESID 36 THROUGH 59 )
67X-RAY DIFFRACTION67CHAIN N AND (RESID 60 THROUGH 73 )
68X-RAY DIFFRACTION68CHAIN N AND (RESID 74 THROUGH 125 )
69X-RAY DIFFRACTION69CHAIN N AND (RESID 126 THROUGH 237 )
70X-RAY DIFFRACTION70CHAIN O AND (RESID 1 THROUGH 35 )
71X-RAY DIFFRACTION71CHAIN O AND (RESID 36 THROUGH 59 )
72X-RAY DIFFRACTION72CHAIN O AND (RESID 60 THROUGH 73 )
73X-RAY DIFFRACTION73CHAIN O AND (RESID 74 THROUGH 96 )
74X-RAY DIFFRACTION74CHAIN O AND (RESID 97 THROUGH 139 )
75X-RAY DIFFRACTION75CHAIN O AND (RESID 140 THROUGH 178 )
76X-RAY DIFFRACTION76CHAIN O AND (RESID 179 THROUGH 205 )
77X-RAY DIFFRACTION77CHAIN O AND (RESID 206 THROUGH 237 )
78X-RAY DIFFRACTION78CHAIN P AND (RESID 5 THROUGH 21 )
79X-RAY DIFFRACTION79CHAIN P AND (RESID 22 THROUGH 34 )
80X-RAY DIFFRACTION80CHAIN P AND (RESID 35 THROUGH 54 )
81X-RAY DIFFRACTION81CHAIN P AND (RESID 55 THROUGH 78 )
82X-RAY DIFFRACTION82CHAIN P AND (RESID 79 THROUGH 92 )
83X-RAY DIFFRACTION83CHAIN P AND (RESID 93 THROUGH 144 )
84X-RAY DIFFRACTION84CHAIN P AND (RESID 145 THROUGH 186 )
85X-RAY DIFFRACTION85CHAIN P AND (RESID 187 THROUGH 229 )
86X-RAY DIFFRACTION86CHAIN P AND (RESID 230 THROUGH 261 )

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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

-
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

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