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- PDB-6ci9: RMM microcompartment-associated aminopropanol dehydrogenase NADP ... -

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基本情報

登録情報
データベース: PDB / ID: 6ci9
タイトルRMM microcompartment-associated aminopropanol dehydrogenase NADP + aminoacetone holo-structure
要素3-oxoacyl-[acyl-carrier-protein] reductase
キーワードOXIDOREDUCTASE / dehydrogenase / short-chain dehydrogenase/reductase
機能・相同性
機能・相同性情報


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
類似検索 - 分子機能
Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
1-aminopropan-2-one / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-oxoacyl-[acyl-carrier-protein] reductase
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: 1.9 Å
データ登録者Mallette, E. / Kimber, M.S.
資金援助 カナダ, 1件
組織認可番号
Natural Sciences and Engineering Research Council (NSERC, Canada)04045-2015 カナダ
引用ジャーナル: Biochemistry / : 2018
タイトル: Structure and Kinetics of the S-(+)-1-Amino-2-propanol Dehydrogenase from the RMM Microcompartment of Mycobacterium smegmatis.
著者: Mallette, E. / Kimber, M.S.
履歴
登録2018年2月23日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年5月30日Provider: repository / タイプ: Initial release
改定 1.12018年7月11日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
改定 1.22019年2月20日Group: Author supporting evidence / Data collection / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32020年1月8日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42023年10月4日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
C: 3-oxoacyl-[acyl-carrier-protein] reductase
D: 3-oxoacyl-[acyl-carrier-protein] reductase
E: 3-oxoacyl-[acyl-carrier-protein] reductase
F: 3-oxoacyl-[acyl-carrier-protein] reductase
G: 3-oxoacyl-[acyl-carrier-protein] reductase
H: 3-oxoacyl-[acyl-carrier-protein] reductase
I: 3-oxoacyl-[acyl-carrier-protein] reductase
J: 3-oxoacyl-[acyl-carrier-protein] reductase
K: 3-oxoacyl-[acyl-carrier-protein] reductase
L: 3-oxoacyl-[acyl-carrier-protein] reductase
M: 3-oxoacyl-[acyl-carrier-protein] reductase
N: 3-oxoacyl-[acyl-carrier-protein] reductase
O: 3-oxoacyl-[acyl-carrier-protein] reductase
P: 3-oxoacyl-[acyl-carrier-protein] reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)442,51873
ポリマ-428,65716
非ポリマー13,86157
45,0012498
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
C: 3-oxoacyl-[acyl-carrier-protein] reductase
D: 3-oxoacyl-[acyl-carrier-protein] reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)110,65619
ポリマ-107,1644
非ポリマー3,49215
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area22390 Å2
ΔGint-217 kcal/mol
Surface area28980 Å2
手法PISA
2
E: 3-oxoacyl-[acyl-carrier-protein] reductase
F: 3-oxoacyl-[acyl-carrier-protein] reductase
G: 3-oxoacyl-[acyl-carrier-protein] reductase
H: 3-oxoacyl-[acyl-carrier-protein] reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)110,62118
ポリマ-107,1644
非ポリマー3,45614
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area21690 Å2
ΔGint-197 kcal/mol
Surface area28850 Å2
手法PISA
3
I: 3-oxoacyl-[acyl-carrier-protein] reductase
J: 3-oxoacyl-[acyl-carrier-protein] reductase
K: 3-oxoacyl-[acyl-carrier-protein] reductase
L: 3-oxoacyl-[acyl-carrier-protein] reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)110,62118
ポリマ-107,1644
非ポリマー3,45614
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area21730 Å2
ΔGint-200 kcal/mol
Surface area28710 Å2
手法PISA
4
M: 3-oxoacyl-[acyl-carrier-protein] reductase
N: 3-oxoacyl-[acyl-carrier-protein] reductase
O: 3-oxoacyl-[acyl-carrier-protein] reductase
P: 3-oxoacyl-[acyl-carrier-protein] reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)110,62118
ポリマ-107,1644
非ポリマー3,45614
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area21760 Å2
ΔGint-199 kcal/mol
Surface area28900 Å2
手法PISA
単位格子
Length a, b, c (Å)131.770, 129.060, 145.790
Angle α, β, γ (deg.)90.000, 107.880, 90.000
Int Tables number4
Space group name H-MP1211

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要素

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タンパク質 , 1種, 16分子 ABCDEFGHIJKLMNOP

#1: タンパク質
3-oxoacyl-[acyl-carrier-protein] reductase


分子量: 26791.045 Da / 分子数: 16 / 由来タイプ: 組換発現
由来: (組換発現) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (バクテリア)
: ATCC 700084 / mc(2)155 / 遺伝子: MSMEG_0269 / プラスミド: pET28a / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3)
参照: UniProt: A0QP46, 3-oxoacyl-[acyl-carrier-protein] reductase

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非ポリマー , 5種, 2555分子

#2: 化合物
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


分子量: 743.405 Da / 分子数: 16 / 由来タイプ: 合成 / : C21H28N7O17P3 / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-F3V / 1-aminopropan-2-one / アミノアセトン


分子量: 73.094 Da / 分子数: 16 / 由来タイプ: 合成 / : C3H7NO / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 17 / 由来タイプ: 合成 / : Cl
#5: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 8 / 由来タイプ: 合成 / : Mg
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2498 / 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: 2.75 Å3/Da / 溶媒含有率: 55.31 %
結晶化温度: 298 K / 手法: 蒸発脱水法 / pH: 8.5 / 詳細: 0.1 M Tris, 0.2 M MgCl2, 13% PEG4000

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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: CLSI / ビームライン: 08ID-1 / 波長: 0.97949 Å
検出器タイプ: RAYONIX MX-300 / 検出器: CCD / 日付: 2016年8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: 0.97949 Å / 相対比: 1
反射解像度: 1.54→48.495 Å / Num. obs: 561674 / % possible obs: 82.2 % / 冗長度: 3.288 % / CC1/2: 0.996 / Rmerge(I) obs: 0.137 / Rrim(I) all: 0.163 / Χ2: 1.003 / Net I/σ(I): 5.88 / Num. measured all: 1847055 / Scaling rejects: 837
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allCC1/2
1.54-1.581.8744.6860.132745550429146486.45929
1.58-1.621.973.4350.193884749139197234.69340.1
1.62-1.672.0642.9060.245119047789247973.92551.90.144
1.67-1.722.1652.4830.36504346455300483.30964.70.177
1.72-1.782.3022.1380.398077744951350882.80178.10.25
1.78-1.842.5931.640.5910124843510390442.08389.70.401
1.84-1.913.2651.3490.9713410741993410791.61997.80.574
1.91-1.993.7931.0341.5815303940462403521.20799.70.767
1.99-2.083.7950.7612.2714667938733386500.88999.80.834
2.08-2.183.8030.5443.1614087137134370410.63599.70.903
2.18-2.33.8040.4034.1813379335250351720.4799.80.94
2.3-2.433.8040.2985.3412673733403333190.34899.70.966
2.43-2.63.8010.2156.911901231387313070.25199.70.978
2.6-2.813.7930.1489.1411059529239291560.17399.70.989
2.81-3.083.7760.09812.0610112726918267810.11499.50.994
3.08-3.443.7430.06716.19047624336241750.07999.30.996
3.44-3.983.6990.0520.737898721551213520.05899.10.997
3.98-4.873.6810.04324.086668218232181140.0599.40.997
4.87-6.893.7080.04123.365207714140140450.04899.30.997
6.89-48.4953.6380.03626.8328313788077830.04298.80.998

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX1.12_2829精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
RESOLVE位相決定
PDB_EXTRACT3.24データ抽出
精密化構造決定の手法: 分子置換
開始モデル: pdbid 3RIH
解像度: 1.9→48.495 Å / SU ML: 0.27 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 29.18 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.233 18113 5 %
Rwork0.2037 344258 -
obs0.2052 362371 99.5 %
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: 140.93 Å2 / Biso mean: 40.8965 Å2 / Biso min: 10.53 Å2
精密化ステップサイクル: final / 解像度: 1.9→48.495 Å
タンパク質核酸リガンド溶媒全体
原子数29712 0 868 2498 33078
Biso mean--34.55 42.24 -
残基数----4088
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00731037
X-RAY DIFFRACTIONf_angle_d0.88242321
X-RAY DIFFRACTIONf_chiral_restr0.0544995
X-RAY DIFFRACTIONf_plane_restr0.0055492
X-RAY DIFFRACTIONf_dihedral_angle_d4.2817935
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92160.4536030.4176114421204599
1.9216-1.94420.41015980.3837114661206499
1.9442-1.96790.3896030.3581114321203599
1.9679-1.99280.3666010.3371140212003100
1.9928-2.0190.33636000.31721144112041100
2.019-2.04670.32846060.31147712083100
2.0467-2.07590.30565970.28021139311990100
2.0759-2.10690.26876020.2607114781208099
2.1069-2.13990.29956040.25861149812102100
2.1399-2.17490.28945990.24841142812027100
2.1749-2.21240.28646050.2481149312098100
2.2124-2.25270.27796010.23471140712008100
2.2527-2.2960.25546070.22931151912126100
2.296-2.34290.2636050.22441150212107100
2.3429-2.39380.2596040.21821144912053100
2.3938-2.44950.2496010.2061143412035100
2.4495-2.51070.23896040.20781147012074100
2.5107-2.57860.23866020.20591147812080100
2.5786-2.65450.24796040.20781147112075100
2.6545-2.74020.24596080.20011153312141100
2.7402-2.83810.23156030.1921145312056100
2.8381-2.95170.21796050.1855114881209399
2.9517-3.0860.2236050.1924114971210299
3.086-3.24870.22336030.1801114471205099
3.2487-3.45220.19356030.1765114681207199
3.4522-3.71860.18996040.17114761208099
3.7186-4.09270.19396040.1586114781208299
4.0927-4.68450.16786070.1508115221212999
4.6845-5.90030.19696100.1646115821219299
5.9003-48.51040.18396150.1735116341224999
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)
12.4698-0.5805-0.14143.05130.8862.7117-0.03120.11230.2020.12870.0605-0.5988-0.17650.357-0.08390.1776-0.0453-0.07010.19720.05240.3577217.441-29.0473202.1295
27.66642.54367.09234.49791.82689.17390.13140.3208-0.1764-0.05630.0168-0.76610.04170.5966-0.17380.16770.01160.01680.26690.01260.3411217.9602-34.2413197.6053
32.2397-1.03161.40931.8088-0.78013.39970.14190.2199-0.128-0.1335-0.122-0.04750.04470.0540.01240.175-0.0162-0.01090.13350.00220.1763204.7959-33.0774192.8524
41.5002-0.74070.97811.0030.15391.26680.04540.1070.0358-0.0817-0.13040.0146-0.02030.07950.08740.1804-0.0345-00.15960.02250.1661200.0068-23.4923198.2466
50.92410.6324-0.80131.0086-0.36955.42950.06030.97320.6219-1.2013-0.1078-0.1549-0.5905-0.09930.06540.91050.0597-0.03830.72640.23030.6836212.5023-9.8393187.1613
62.6549-1.3410.59452.05490.47620.5733-0.07240.1710.22390.038-0.0126-0.4724-0.08660.09870.08560.2387-0.0534-0.10010.15850.01370.2277205.4278-15.0425204.4228
73.7972.23161.19564.06935.08777.3483-0.1352-0.2346-0.11640.35960.2656-0.3440.23320.5358-0.2120.4850.0196-0.32940.30920.01990.5262217.2574-15.7931217.8424
82.9001-0.05241.23250.7181-0.01270.5230.0132-0.2986-0.09980.25930.0613-0.10320.198-0.0131-0.07240.65290.0359-0.31740.2842-0.0190.2728203.7266-12.191227.0348
91.3047-1.069-0.98931.62771.38742.9821-0.046-0.1810.04440.03160.03590.0077-0.1789-0.08020.0610.53010.0443-0.31960.3178-0.05360.3327204.8327-6.4429229.7884
104.3318-2.10612.35412.1146-1.90432.475-0.0005-0.5339-0.21620.1750.18860.00830.2155-0.1465-0.17170.82040.1301-0.23470.55910.03190.314200.1667-9.6246238.6897
113.2657-1.70912.08852.4587-1.30743.4309-0.0646-0.25760.03790.180.0062-0.10240.02460.15780.04150.65640.0642-0.28850.4184-0.00210.3064204.7223-6.049232.1643
122.5570.22020.99630.56280.17440.8168-0.1239-0.32120.23630.37770.0056-0.0184-0.2009-0.14260.16180.53620.0463-0.31570.2131-0.06810.3146196.1248-0.0549222.653
131.8918-0.62510.88461.64950.46791.2115-0.2732-0.16050.18710.20790.0166-0.0886-0.1435-0.04830.23560.34950.0108-0.13630.1503-0.01910.1999194.1511-6.321212.7241
144.81722.08892.70356.17770.31511.8070.2138-0.95540.19570.8471-0.17680.54050.01-0.6774-0.09040.4538-0.0138-0.14470.3577-0.05920.3018194.2454-13.9564220.4783
152.34150.64980.85514.96282.5067.2445-0.0466-0.7461-0.19910.8833-0.10691.14350.4023-1.48850.20240.5056-0.06630.08470.54170.08560.461186.0807-26.0806221.1418
161.2351-0.2888-0.19732.1811-0.1372.6107-0.1735-0.03360.25390.2570.1173-0.32980.01230.10370.04620.27-0.0418-0.12750.14270.01150.2598205.0057-14.4111212.8234
176.50620.77782.11534.81792.77693.35860.3298-0.8131-0.69930.5002-0.1891.00481.1034-1.036-0.10310.325-0.0862-0.02750.2550.06180.4059185.5274-25.5669209.729
184.993-3.6177-5.26515.61254.04575.56940.10110.8327-0.1208-0.7835-0.40030.6012-0.2485-0.90570.30310.45160.0627-0.30030.4051-0.1420.7008162.1109-5.206189.8021
191.9951-0.27220.4770.1430.36241.8306-0.21990.10770.1141-0.4217-0.14330.5234-0.3803-0.18840.3590.43240.0789-0.26720.2395-0.08890.4887170.19188.8617197.5646
202.59311.05021.42576.83634.82025.0536-0.32830.0620.5476-0.4414-0.10270.2675-0.8405-0.14150.4120.51670.0842-0.29340.2363-0.06650.5558170.20120.3194198.4718
212.34280.03920.56911.2837-0.30561.4172-0.1898-0.09160.1314-0.0038-0.03240.3688-0.316-0.29120.19440.39560.0784-0.23550.2192-0.11180.4376172.57229.4599205.6183
222.1753-0.55590.12642.04170.28681.971-0.2356-0.0420.19910.0553-0.03040.2301-0.2832-0.19860.21860.30440.0364-0.1390.1385-0.02770.2689180.42760.5383205.8476
230.7874-1.2296-0.17132.1251-0.47132.8859-0.07340.14870.2511-0.3246-0.18190.0735-0.3019-0.00060.23530.33490.0062-0.17260.1983-0.00270.2947182.0418-1.0522192.104
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1109.9069-4.1952-7.33072.89783.81225.88140.10.6439-0.0881-0.4629-0.44850.6763-0.3503-0.7850.33440.43850.0149-0.22520.54260.00850.954396.5596-10.2744190.1353
1112.0346-0.22330.42411.38530.83252.1914-0.00910.06360.0215-0.236-0.26240.2623-0.2522-0.36670.24950.45350.0242-0.23330.419-0.06540.7767104.54792.8458197.1886
1120.20280.35761.22843.53262.79157.5676-0.17740.02790.2749-0.0853-0.01880.0069-0.3294-0.03340.18290.5090.0825-0.28810.5305-0.06630.9307104.506414.1695198.0877
1131.65040.499-0.57352.259-0.28112.0069-0.02620.02820.0437-0.0341-0.12580.1906-0.2874-0.35010.14570.38780.0421-0.19760.3758-0.08360.7058106.7813.4372205.315
1141.86360.01880.13812.19060.33112.3843-0.2885-0.06970.40540.0568-0.0164-0.0135-0.2632-0.11070.30260.2859-0.0228-0.11680.3333-0.00930.5632114.0691-6.5713208.0484
1151.2785-0.6053-0.64332.9545-0.38443.6473-0.11570.14550.5586-0.2098-0.2526-0.1753-0.41880.07540.34830.3057-0.0271-0.12980.35030.05580.6326118.0221-5.9765193.3064
1162.7883-1.7335-0.18725.1090.23382.68810.02230.19110.097-0.5652-0.27780.8713-0.2474-0.61340.23730.40020.0183-0.15680.5607-0.02280.4972104.8753-21.318180.2906
1174.1876-2.2689-0.12935.10.31311.85050.14670.1178-0.3361-0.4874-0.30310.75590.3576-0.54160.14540.606-0.0443-0.27730.5903-0.04240.5941104.6305-34.1554175.3196
1185.9052-3.35091.34043.241-0.95443.60860.35350.5792-0.5745-0.6259-0.36590.72910.1634-0.54550.02670.5611-0.0074-0.18840.4574-0.09970.6112107.0946-31.1769173.6663
1192.6687-1.44910.46454.5829-1.58352.79090.15030.3145-0.2471-0.4981-0.06640.2670.0799-0.3384-0.11280.328-0.0266-0.07190.3766-0.02310.4441117.4488-32.6895178.6808
1204.7982-4.61263.35714.5297-3.00592.87540.12380.1178-0.1943-0.285-0.10960.26340.2524-0.1331-0.01580.3089-0.00620.00480.41710.0270.453124.5235-35.2087182.4198
1211.1757-0.8710.94051.2777-0.29891.00280.060.14250.092-0.162-0.1962-0.0277-0.11110.13030.09530.2319-0.0710.11570.4610.08660.4219121.6969-24.4559186.421
1223.3549-1.0524-0.32441.0962-0.53384.9867-0.04440.1951-0.612-0.2596-0.0280.37350.6125-0.58570.04030.3712-0.0433-0.10090.4531-0.07190.5338111.8882-29.4266190.3751
1233.78211.171-0.46221.02611.04742.2061-0.07560.0214-0.2414-0.1141-0.15030.11830.3684-0.21580.2010.26730.0153-0.05490.36080.00230.479108.9176-23.9205194.0243
1244.35750.32564.20191.08542.05766.91580.2769-0.3699-0.1960.08120.06720.33230.8197-1.0632-0.33930.2382-0.0426-0.01130.3237-0.00650.5124113.3392-24.5122203.9169
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 50 )A-1 - 50
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 67 )A51 - 67
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 133 )A68 - 133
4X-RAY DIFFRACTION4chain 'A' and (resid 134 through 192 )A134 - 192
5X-RAY DIFFRACTION5chain 'A' and (resid 193 through 209 )A193 - 209
6X-RAY DIFFRACTION6chain 'A' and (resid 210 through 253 )A210 - 253
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 8 )B0 - 8
8X-RAY DIFFRACTION8chain 'B' and (resid 9 through 30 )B9 - 30
9X-RAY DIFFRACTION9chain 'B' and (resid 31 through 39 )B31 - 39
10X-RAY DIFFRACTION10chain 'B' and (resid 40 through 50 )B40 - 50
11X-RAY DIFFRACTION11chain 'B' and (resid 51 through 67 )B51 - 67
12X-RAY DIFFRACTION12chain 'B' and (resid 68 through 133 )B68 - 133
13X-RAY DIFFRACTION13chain 'B' and (resid 134 through 178 )B134 - 178
14X-RAY DIFFRACTION14chain 'B' and (resid 179 through 199 )B179 - 199
15X-RAY DIFFRACTION15chain 'B' and (resid 200 through 217 )B200 - 217
16X-RAY DIFFRACTION16chain 'B' and (resid 218 through 243 )B218 - 243
17X-RAY DIFFRACTION17chain 'B' and (resid 244 through 254 )B244 - 254
18X-RAY DIFFRACTION18chain 'C' and (resid 0 through 8 )C0 - 8
19X-RAY DIFFRACTION19chain 'C' and (resid 9 through 40 )C9 - 40
20X-RAY DIFFRACTION20chain 'C' and (resid 41 through 49 )C41 - 49
21X-RAY DIFFRACTION21chain 'C' and (resid 50 through 104 )C50 - 104
22X-RAY DIFFRACTION22chain 'C' and (resid 105 through 199 )C105 - 199
23X-RAY DIFFRACTION23chain 'C' and (resid 200 through 243 )C200 - 243
24X-RAY DIFFRACTION24chain 'C' and (resid 244 through 256 )C244 - 256
25X-RAY DIFFRACTION25chain 'D' and (resid -1 through 50 )D-1 - 50
26X-RAY DIFFRACTION26chain 'D' and (resid 51 through 104 )D51 - 104
27X-RAY DIFFRACTION27chain 'D' and (resid 105 through 243 )D105 - 243
28X-RAY DIFFRACTION28chain 'D' and (resid 244 through 256 )D244 - 256
29X-RAY DIFFRACTION29chain 'E' and (resid -1 through 8 )E-1 - 8
30X-RAY DIFFRACTION30chain 'E' and (resid 9 through 39 )E9 - 39
31X-RAY DIFFRACTION31chain 'E' and (resid 40 through 50 )E40 - 50
32X-RAY DIFFRACTION32chain 'E' and (resid 51 through 67 )E51 - 67
33X-RAY DIFFRACTION33chain 'E' and (resid 68 through 82 )E68 - 82
34X-RAY DIFFRACTION34chain 'E' and (resid 83 through 104 )E83 - 104
35X-RAY DIFFRACTION35chain 'E' and (resid 105 through 133 )E105 - 133
36X-RAY DIFFRACTION36chain 'E' and (resid 134 through 178 )E134 - 178
37X-RAY DIFFRACTION37chain 'E' and (resid 179 through 199 )E179 - 199
38X-RAY DIFFRACTION38chain 'E' and (resid 200 through 217 )E200 - 217
39X-RAY DIFFRACTION39chain 'E' and (resid 218 through 243 )E218 - 243
40X-RAY DIFFRACTION40chain 'E' and (resid 244 through 256 )E244 - 256
41X-RAY DIFFRACTION41chain 'F' and (resid 0 through 50 )F0 - 50
42X-RAY DIFFRACTION42chain 'F' and (resid 51 through 67 )F51 - 67
43X-RAY DIFFRACTION43chain 'F' and (resid 68 through 104 )F68 - 104
44X-RAY DIFFRACTION44chain 'F' and (resid 105 through 192 )F105 - 192
45X-RAY DIFFRACTION45chain 'F' and (resid 193 through 209 )F193 - 209
46X-RAY DIFFRACTION46chain 'F' and (resid 210 through 253 )F210 - 253
47X-RAY DIFFRACTION47chain 'G' and (resid -1 through 29 )G-1 - 29
48X-RAY DIFFRACTION48chain 'G' and (resid 30 through 50 )G30 - 50
49X-RAY DIFFRACTION49chain 'G' and (resid 51 through 67 )G51 - 67
50X-RAY DIFFRACTION50chain 'G' and (resid 68 through 104 )G68 - 104
51X-RAY DIFFRACTION51chain 'G' and (resid 105 through 178 )G105 - 178
52X-RAY DIFFRACTION52chain 'G' and (resid 179 through 199 )G179 - 199
53X-RAY DIFFRACTION53chain 'G' and (resid 200 through 243 )G200 - 243
54X-RAY DIFFRACTION54chain 'G' and (resid 244 through 256 )G244 - 256
55X-RAY DIFFRACTION55chain 'H' and (resid 0 through 8 )H0 - 8
56X-RAY DIFFRACTION56chain 'H' and (resid 9 through 40 )H9 - 40
57X-RAY DIFFRACTION57chain 'H' and (resid 41 through 49 )H41 - 49
58X-RAY DIFFRACTION58chain 'H' and (resid 50 through 82 )H50 - 82
59X-RAY DIFFRACTION59chain 'H' and (resid 83 through 116 )H83 - 116
60X-RAY DIFFRACTION60chain 'H' and (resid 117 through 187 )H117 - 187
61X-RAY DIFFRACTION61chain 'H' and (resid 188 through 199 )H188 - 199
62X-RAY DIFFRACTION62chain 'H' and (resid 200 through 243 )H200 - 243
63X-RAY DIFFRACTION63chain 'H' and (resid 244 through 256 )H244 - 256
64X-RAY DIFFRACTION64chain 'I' and (resid 0 through 8 )I0 - 8
65X-RAY DIFFRACTION65chain 'I' and (resid 9 through 39 )I9 - 39
66X-RAY DIFFRACTION66chain 'I' and (resid 40 through 50 )I40 - 50
67X-RAY DIFFRACTION67chain 'I' and (resid 51 through 104 )I51 - 104
68X-RAY DIFFRACTION68chain 'I' and (resid 105 through 199 )I105 - 199
69X-RAY DIFFRACTION69chain 'I' and (resid 200 through 239 )I200 - 239
70X-RAY DIFFRACTION70chain 'I' and (resid 240 through 257 )I240 - 257
71X-RAY DIFFRACTION71chain 'J' and (resid 0 through 30 )J0 - 30
72X-RAY DIFFRACTION72chain 'J' and (resid 31 through 50 )J31 - 50
73X-RAY DIFFRACTION73chain 'J' and (resid 51 through 67 )J51 - 67
74X-RAY DIFFRACTION74chain 'J' and (resid 68 through 104 )J68 - 104
75X-RAY DIFFRACTION75chain 'J' and (resid 105 through 178 )J105 - 178
76X-RAY DIFFRACTION76chain 'J' and (resid 179 through 243 )J179 - 243
77X-RAY DIFFRACTION77chain 'J' and (resid 244 through 256 )J244 - 256
78X-RAY DIFFRACTION78chain 'K' and (resid -1 through 29 )K-1 - 29
79X-RAY DIFFRACTION79chain 'K' and (resid 30 through 82 )K30 - 82
80X-RAY DIFFRACTION80chain 'K' and (resid 83 through 116 )K83 - 116
81X-RAY DIFFRACTION81chain 'K' and (resid 117 through 178 )K117 - 178
82X-RAY DIFFRACTION82chain 'K' and (resid 179 through 239 )K179 - 239
83X-RAY DIFFRACTION83chain 'K' and (resid 240 through 253 )K240 - 253
84X-RAY DIFFRACTION84chain 'L' and (resid 0 through 50 )L0 - 50
85X-RAY DIFFRACTION85chain 'L' and (resid 51 through 67 )L51 - 67
86X-RAY DIFFRACTION86chain 'L' and (resid 68 through 104 )L68 - 104
87X-RAY DIFFRACTION87chain 'L' and (resid 105 through 116 )L105 - 116
88X-RAY DIFFRACTION88chain 'L' and (resid 117 through 133 )L117 - 133
89X-RAY DIFFRACTION89chain 'L' and (resid 134 through 192 )L134 - 192
90X-RAY DIFFRACTION90chain 'L' and (resid 193 through 209 )L193 - 209
91X-RAY DIFFRACTION91chain 'L' and (resid 210 through 252 )L210 - 252
92X-RAY DIFFRACTION92chain 'M' and (resid 0 through 50 )M0 - 50
93X-RAY DIFFRACTION93chain 'M' and (resid 51 through 67 )M51 - 67
94X-RAY DIFFRACTION94chain 'M' and (resid 68 through 133 )M68 - 133
95X-RAY DIFFRACTION95chain 'M' and (resid 134 through 178 )M134 - 178
96X-RAY DIFFRACTION96chain 'M' and (resid 179 through 199 )M179 - 199
97X-RAY DIFFRACTION97chain 'M' and (resid 200 through 217 )M200 - 217
98X-RAY DIFFRACTION98chain 'M' and (resid 218 through 253 )M218 - 253
99X-RAY DIFFRACTION99chain 'N' and (resid 0 through 8 )N0 - 8
100X-RAY DIFFRACTION100chain 'N' and (resid 9 through 39 )N9 - 39
101X-RAY DIFFRACTION101chain 'N' and (resid 40 through 50 )N40 - 50
102X-RAY DIFFRACTION102chain 'N' and (resid 51 through 82 )N51 - 82
103X-RAY DIFFRACTION103chain 'N' and (resid 83 through 104 )N83 - 104
104X-RAY DIFFRACTION104chain 'N' and (resid 105 through 116 )N105 - 116
105X-RAY DIFFRACTION105chain 'N' and (resid 117 through 154 )N117 - 154
106X-RAY DIFFRACTION106chain 'N' and (resid 155 through 187 )N155 - 187
107X-RAY DIFFRACTION107chain 'N' and (resid 188 through 199 )N188 - 199
108X-RAY DIFFRACTION108chain 'N' and (resid 200 through 239 )N200 - 239
109X-RAY DIFFRACTION109chain 'N' and (resid 240 through 253 )N240 - 253
110X-RAY DIFFRACTION110chain 'O' and (resid 1 through 8 )O1 - 8
111X-RAY DIFFRACTION111chain 'O' and (resid 9 through 40 )O9 - 40
112X-RAY DIFFRACTION112chain 'O' and (resid 41 through 49 )O41 - 49
113X-RAY DIFFRACTION113chain 'O' and (resid 50 through 104 )O50 - 104
114X-RAY DIFFRACTION114chain 'O' and (resid 105 through 178 )O105 - 178
115X-RAY DIFFRACTION115chain 'O' and (resid 179 through 252 )O179 - 252
116X-RAY DIFFRACTION116chain 'P' and (resid -1 through 29 )P-1 - 29
117X-RAY DIFFRACTION117chain 'P' and (resid 30 through 50 )P30 - 50
118X-RAY DIFFRACTION118chain 'P' and (resid 51 through 67 )P51 - 67
119X-RAY DIFFRACTION119chain 'P' and (resid 68 through 104 )P68 - 104
120X-RAY DIFFRACTION120chain 'P' and (resid 105 through 125 )P105 - 125
121X-RAY DIFFRACTION121chain 'P' and (resid 126 through 178 )P126 - 178
122X-RAY DIFFRACTION122chain 'P' and (resid 179 through 199 )P179 - 199
123X-RAY DIFFRACTION123chain 'P' and (resid 200 through 239 )P200 - 239
124X-RAY DIFFRACTION124chain 'P' and (resid 240 through 253 )P240 - 253

+
万見について

-
お知らせ

-
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://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