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- PDB-3rbm: Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate... -

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基本情報

登録情報
データベース: PDB / ID: 3rbm
タイトルCrystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH -703
要素Farnesyl pyrophosphate synthase
キーワードTRANSFERASE/TRANSFERASE INHIBITOR / ALPHA-HELICES / ISOPRENE BIOSYNTHESIS / TRANSFERASE-TRANSFERASE INHIBITOR complex
機能・相同性
機能・相同性情報


prenyltransferase activity / isoprenoid biosynthetic process / membrane / metal ion binding
類似検索 - 分子機能
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
Chem-B73 / Farnesyl pyrophosphate synthase, putative
類似検索 - 構成要素
生物種Plasmodium vivax (マラリア 病原虫)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.61 Å
データ登録者Liu, Y.L. / No, J.H. / Oldfield, E.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / : 2012
タイトル: Lipophilic analogs of zoledronate and risedronate inhibit Plasmodium geranylgeranyl diphosphate synthase (GGPPS) and exhibit potent antimalarial activity.
著者: No, J.H. / de Macedo Dossin, F. / Zhang, Y. / Liu, Y.L. / Zhu, W. / Feng, X. / Yoo, J.A. / Lee, E. / Wang, K. / Hui, R. / Freitas-Junior, L.H. / Oldfield, E.
履歴
登録2011年3月29日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02012年2月29日Provider: repository / タイプ: Initial release
改定 1.12012年5月23日Group: Database references
改定 1.22023年9月13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 / struct_ref_seq_dif / struct_site
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_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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_label_seq_id / _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_label_seq_id / _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_ref_seq_dif.details / _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: Farnesyl pyrophosphate synthase
B: Farnesyl pyrophosphate synthase
C: Farnesyl pyrophosphate synthase
D: Farnesyl pyrophosphate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)187,24124
ポリマ-184,8634
非ポリマー2,37820
4,792266
1
A: Farnesyl pyrophosphate synthase
B: Farnesyl pyrophosphate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,62012
ポリマ-92,4322
非ポリマー1,18910
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-139 kcal/mol
Surface area28120 Å2
手法PISA
2
C: Farnesyl pyrophosphate synthase
D: Farnesyl pyrophosphate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,62012
ポリマ-92,4322
非ポリマー1,18910
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-138 kcal/mol
Surface area27800 Å2
手法PISA
単位格子
Length a, b, c (Å)107.682, 107.952, 140.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21B
31C
41D

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要素

#1: タンパク質
Farnesyl pyrophosphate synthase


分子量: 46215.750 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Plasmodium vivax (マラリア 病原虫)
: Salvador I / 遺伝子: PVX_092040 / プラスミド: P15-TEV-LIC / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): DH5A / 参照: UniProt: A5K4U6
#2: 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: 12 / 由来タイプ: 合成 / : Mg
#3: 化合物
ChemComp-B73 / 3-(2,2-diphosphonoethyl)-1-dodecyl-1H-imidazol-3-ium


分子量: 425.417 Da / 分子数: 4 / 由来タイプ: 合成 / : C17H35N2O6P2
#4: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 4 / 由来タイプ: 合成 / : SO4
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 266 / 由来タイプ: 天然 / : H2O
配列の詳細AUTHORS STATE THAT THE SEQUENCE IN THIS STUDY HAS BEEN CONFIRMED BY CDNA SEQUENCING

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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: 2.21 Å3/Da / 溶媒含有率: 44.39 %
結晶化pH: 8.5
詳細: 100MM TRIS, 200MM LITHIUM SULFATE, 22% PEG 3,350, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

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データ収集

回折平均測定温度: 298 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 21-ID-D / 波長: 0.97856
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2010年3月14日 / 詳細: SI(111) DOUBLE CRYSTAL MONOCHROMETER
放射モノクロメーター: SI(111) / 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: 0.97856 Å / 相対比: 1
反射解像度: 2.6→50 Å / Num. obs: 50497 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / 冗長度: 6.1 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 28.88
反射 シェル解像度: 2.6→2.64 Å / 冗長度: 6.2 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 7.29 / % possible all: 99.6

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解析

ソフトウェア
名称バージョン分類
PHASES位相決定
REFMAC5.5.0109精密化
HKL-2000データ削減
HKL-2000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: PDB ENTRY 3EZ3
解像度: 2.61→45.58 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.896 / SU B: 22.209 / SU ML: 0.238 / 交差検証法: THROUGHOUT / ESU R Free: 0.337 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.253 2554 5.1 %RANDOM
Rwork0.208 ---
obs0.21 47716 99.2 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 33.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.19 Å2
精密化ステップサイクル: LAST / 解像度: 2.61→45.58 Å
タンパク質核酸リガンド溶媒全体
原子数11619 0 140 266 12025
拘束条件
Refine-IDタイプDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211929
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.96516137
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85951417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56425.018552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.601152097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.4571529
X-RAY DIFFRACTIONr_chiral_restr0.0870.21805
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.028799
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3081.57097
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.454211453
X-RAY DIFFRACTIONr_scbond_it2.91534832
X-RAY DIFFRACTIONr_scangle_it4.7814.54684
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDタイプRms dev position (Å)Weight position
1A1407tight positional0.110.05
2B1407tight positional0.120.05
3C1407tight positional0.10.05
4D1407tight positional0.10.05
1A1446loose positional0.135
2B1446loose positional0.145
3C1446loose positional0.125
4D1446loose positional0.135
1A1407tight thermal0.410.5
2B1407tight thermal0.360.5
3C1407tight thermal0.360.5
4D1407tight thermal0.350.5
1A1446loose thermal0.4210
2B1446loose thermal0.4110
3C1446loose thermal0.3810
4D1446loose thermal0.3910
LS精密化 シェル解像度: 2.61→2.67 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.322 187 -
Rwork0.274 3354 -
obs--96.46 %
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)
131.0383-26.7996-29.63823.141825.592228.3033.70431.97232.1834-3.145-1.6491-1.9157-3.4612-1.8717-2.05531.06990.45520.27410.20480.11460.6751-16.2992-1.008-25.0583
20.0119-0.01650.25380.105-0.88768.9527-0.003-0.0263-0.0236-0.0225-0.0886-0.04720.18270.20710.09160.26940.0515-0.00470.30760.05370.3561-17.1348-2.1515-10.0592
32.80161.1082-0.13181.0932-0.8885.8910.063-0.2437-0.1847-0.1102-0.0999-0.16980.29390.02220.03690.27550.05180.00050.27050.02880.3024-20.7359-7.82673.104
40.1830.2767-0.13210.4324-0.21750.126-0.05040.00180.0123-0.06820.04160.01840.0689-0.03810.00880.32570.01320.01380.299-0.01990.2954-24.34982.1474-18.7647
52.9466-2.46891.10323.3652-2.70962.88080.05460.02550.1065-0.1656-0.2727-0.23680.18320.40380.21810.2505-0.00970.04320.3305-0.00170.3033-7.17658.6525-26.1531
60.22190.1205-0.17090.3170.0280.3944-0.00120.02420.0188-0.00560.01060.01340.0584-0.0066-0.00940.30360.00930.00230.29880.00730.2979-30.20923.6372-11.8026
74.52991.40735.18122.4227-0.47748.9232-0.09810.11970.01680.19830.1408-0.1401-0.03380.2094-0.04270.25220.00450.00130.34990.00660.2997-6.966314.4792-11.1134
83.8573-0.94980.36750.2371-0.0910.05230.0105-0.13110.0034-0.01560.00980.0118-0.05920.0044-0.02020.3196-0.00990.00850.30070.01050.2952-31.690519.1159-12.5086
91.37161.6482-0.73472.7313-0.0721.3041-0.0011-0.02080.2368-0.07920.01730.3144-0.14090.0092-0.01620.26020.0502-0.04520.2884-0.00110.3363-51.664821.3132-1.497
103.18042.5872-4.10483.5246-3.2016.3325-0.06610.1667-0.012-0.0780.09310.1449-0.1727-0.273-0.0270.26020.049-0.02160.24760.01740.289-51.859922.9959-18.7263
112.6014-0.5381-0.85920.11140.17820.2941-0.0021-0.01690.063-0.00140.0057-0.0116-0.04990.0231-0.00360.3065-0.01070.0120.2950.0030.3092-27.430619.2324-21.6919
121.81181.0405-0.69772.1011-1.25540.75590.1398-0.21110.28590.0786-0.0830.0754-0.06160.0431-0.05680.3102-0.01060.01560.2649-0.0330.2997-18.325625.6424-25.1116
132.21591.93180.02651.70250.0040.09470.0269-0.0763-0.1015-0.0354-0.038-0.05090.15320.07930.01110.3237-0.00180.00410.30.01230.2905-37.555114.2001-29.1132
142.62280.2364-1.77880.0225-0.16511.2542-0.17390.3242-0.3099-0.03610.0103-0.01990.1547-0.0790.16360.46580.0748-0.07220.4778-0.07770.348-43.03341.1901-31.1656
150.0422-0.02340.08920.0942-0.01460.2323-0.036-0.0388-0.01420.10870.0642-0.10730.0307-0.0946-0.02820.29130.00120.0040.30430.0150.3203-47.640613.5301-24.6711
163.8063-1.0120.43830.47380.65253.03610.03090.15360.2680.0033-0.0599-0.06320.051-0.22450.0290.25860.0232-0.01070.29970.01860.2739-59.499621.5858-28.9546
171.5168-0.7571-0.77350.52990.04321.4207-0.1495-0.0176-0.26530.00460.03310.11660.01530.03630.11640.2839-0.00750.0090.30330.02030.3028-56.757511.4192-27.7768
1811.94453.8497-0.31861.2963-0.4181.9411-0.11670.43260.1432-0.08370.0590.04310.34090.24410.05770.30770.01380.00770.3526-0.03090.2247-43.49215.7308-38.0081
190.710.6045-0.45110.5639-0.37960.3027-0.07880.17730.0603-0.06050.1363-0.06150.0117-0.0568-0.05750.3192-0.04220.0210.32320.02910.2706-22.969320.5987-36.7991
203.78236.0457-1.093710.0523-0.5354.1138-0.06140.22290.32340.0950.18590.51320.6798-0.6217-0.12450.3256-0.10560.0050.30440.06490.2265-27.106810.2691-34.8215
211.37954.16960.487312.89063.838819.68350.16060.0155-0.00850.4230.0453-0.0552-0.6271-0.088-0.2060.12760.06070.00130.2038-0.11530.3309-26.626630.453714.6309
220.4597-0.41091.1960.75690.3448.3442-0.09430.0670.04870.0456-0.10550.0106-0.27-0.0520.19980.3144-0.03470.00320.24630.01860.3306-29.889629.9613-0.054
232.6249-0.25940.38431.8753-0.04112.1030.05-0.03070.17610.02720.04260.0723-0.12780.0671-0.09270.3058-0.01840.00570.241-0.00830.3148-37.648530.7186-12.4313
240.66290.0815-0.19760.0345-0.07630.1867-0.0024-0.14650.0644-0.028-0.0207-0.0070.0615-0.01880.02310.3254-0.0324-0.01240.297-0.02820.3046-32.453122.10248.4397
251.6567-0.8461.37342.67402.6999-0.1701-0.04050.17040.07030.0168-0.3305-0.02490.01150.15330.2017-0.0566-0.01290.21430.00990.3136-13.187729.089114.2
260.68380.1566-0.02380.12830.02090.18170.0272-0.0484-0.0332-0.0014-0.0175-0.0014-0.0111-0.0241-0.00970.309-0.016-0.00390.3043-0.00140.2884-34.534616.66292.8068
270.51550.9934-0.23892.0186-0.34250.26760.01840.00930.01070.03630.03530.02610.02770.0667-0.05360.2937-0.0134-0.00920.31150.01620.3094-22.60477.91212.2812
284.8779-2.4030.15761.32680.55982.85630.0108-0.0293-0.34850.05540.04760.16910.31950.1604-0.05840.39820.0012-0.02660.20510.0110.324-32.1972-15.5463-0.2871
290.35650.41850.79790.78490.64632.0938-0.0019-0.1009-0.0048-0.1728-0.0179-0.0740.2416-0.30750.01980.33740.0131-0.01930.26960.0170.3072-40.2853-11.4549-9.1429
306.6377-1.48522.50940.6627-1.37213.8472-0.0366-0.0932-0.231-0.1981-0.0314-0.01930.1037-0.09020.0680.3771-0.00640.01730.22370.01840.2557-35.1595-12.093811.0804
310.77621.01780.2331.35690.36840.2660.0617-0.1028-0.04780.0609-0.0917-0.04920.0060.04070.030.302-0.0216-0.00630.32820.01940.3046-21.20687.422711.5021
320.96210.1470.56250.10880.02291.9063-0.0001-0.1186-0.0433-0.1008-0.0005-0.17380.18220.23340.00060.2747-0.01220.06780.31580.02820.4469-8.960711.086413.2849
330.07660.1090.07270.34770.21120.13870.10680.0377-0.02680.1241-0.1350.02850.0481-0.03610.02820.3491-0.042-0.00960.33150.01470.2925-33.49376.216420.8041
340.7519-1.00020.13461.3723-0.20270.04180.02870.03140.01780.063-0.02850.0226-0.0547-0.0299-0.00020.3107-0.041600.32070.00380.3038-38.8395-1.063315.5701
350.2437-0.6607-1.1548.39790.97776.2041-0.0308-0.0256-0.00070.169-0.0041-0.29090.2070.13570.0350.3157-0.0447-0.01960.24730.05760.2411-38.3035-15.056223.3056
360.2449-0.3441-0.3851.85820.06140.8134-0.00190.0349-0.0439-0.0089-0.13260.1139-0.0361-0.0770.13450.3202-0.0437-0.0230.3246-0.00150.2831-45.309-7.622920.5957
370.4871.51460.05715.3648-0.48434.29980.2455-0.14060.06320.5651-0.13980.4048-0.06510.2268-0.10570.3403-0.1235-0.0060.34640.03410.2402-32.1311-0.082429.6268
386.17211.6235-1.69320.5661-0.78462.49740.1561-0.2828-0.18760.1572-0.0856-0.179-0.0003-0.0657-0.07040.3273-0.0604-0.12820.31090.06890.3621-16.9836.406127.234
397.6633-1.2662-0.55862.18860.02930.76460.10620.04430.07640.2905-0.1882-0.3485-0.0014-0.11940.0820.2928-0.0868-0.05130.28890.00290.2773-15.003816.656624.5858
405.0852-6.44267.468425.1381-11.867211.3094-0.2793-0.52210.31590.7699-0.01720.7869-0.4679-0.67560.29650.2053-0.09340.02990.3072-0.04510.3008-29.037716.124623.957
4110.5266-12.086912.279613.8806-14.100914.33011.20131.29380.5177-1.5356-1.6212-0.5691.54221.48850.41990.35340.3627-0.06890.46230.17480.8433-96.03864.5304-13.788
420.4565-0.72030.89081.5518-0.25125.0527-0.0317-0.02870.03960.06890.0342-0.0227-0.0855-0.1012-0.00240.2520.02670.04690.31130.02270.3885-92.10433.45980.5744
431.7207-0.2816-0.45292.13741.21235.76060.0003-0.03990.1080.21280.0825-0.0453-0.2172-0.1372-0.08280.30270.00950.0190.2430.00320.3599-85.88446.949313.513
440.57330.66690.20170.78290.17480.8539-0.04690.0550.0556-0.03050.07290.0581-0.03430.034-0.0260.28190.0270.0040.28810.01770.3657-86.82540.7523-9.7064
450.4741.11110.7573.34524.504211.9818-0.2067-0.0730.2332-0.4035-0.1570.5532-0.34490.1420.36380.23080.0324-0.06210.33080.00690.4703-104.8401-5.0078-14.1253
460.73770.3918-0.12940.4207-0.17860.1378-0.04860.02820.03260.00790.06030.0463-0.01270.0018-0.01170.30360.00050.01130.2917-0.00030.3267-79.8544-1.7877-4.5034
472.3685-0.2283-0.68090.15060.1630.53850.0733-0.0008-0.054-0.0349-0.0410.06140.0897-0.0129-0.03230.3083-0.01520.02070.28560.01120.3075-81.6764-16.4423-6.8436
484.39593.42894.48832.69033.50734.59-0.37020.4774-0.1012-0.31620.4358-0.0736-0.36520.5244-0.06560.32890.00280.05550.36530.01630.3517-56.2355-20.1321-1.2774
496.1644.75994.349917.44017.04784.06610.4186-0.5309-0.22060.3127-0.1408-0.72180.3274-0.2661-0.27780.28830.05860.06850.39010.02230.2432-57.6121-18.8211-16.4283
502.2934-0.252-0.65820.30690.06290.2146-0.02550.06240.0621-0.08040.03260.030.0949-0.0475-0.00710.3407-0.01570.00750.31440.0130.2922-81.6907-16.2092-17.1273
513.24190.2647-1.27050.56890.52891.5638-0.2233-0.13790.0122-0.11980.14630.11480.2050.05350.07690.2985-0.0346-0.02750.29060.04060.2985-93.7087-21.0046-18.6141
521.82671.021-0.30721.4195-0.10280.0581-0.02030.1550.05290.05120.02480.05430.0214-0.0217-0.00450.3264-0.0252-0.00630.31740.03250.2854-74.2192-6.3122-24.8746
530.1875-0.1959-0.11270.3641-0.12670.4547-0.0339-0.01920.02840.04190.0118-0.01980.00780.0550.02210.3028-0.01340.00490.31630.00240.3139-66.7103-6.277-20.886
541.5205-1.82370.49832.5529-1.14651.0104-0.020.1026-0.0823-0.0697-0.00460.0520.1607-0.06550.02460.29620.02110.04810.3336-0.02050.254-56.5949-16.1268-29.9531
554.1112-0.01941.5470.2591-1.17646.1541-0.13370.17570.1255-0.0180.0146-0.07060.00230.15030.11910.2740.01120.03010.29470.0190.327-55.8771-5.4023-23.8164
562.8527-0.4461-5.06871.89261.10869.78340.06860.55620.0714-0.0175-0.0337-0.318-0.0232-0.3527-0.03490.29930.03450.05230.67170.09440.2774-61.4702-8.8769-35.3546
5723.58522.3277-10.52980.8156-2.820410.13220.03160.42830.378-0.05530.0688-0.0040.1673-0.3182-0.10040.2705-0.0123-0.01880.33390.00890.2643-72.253-9.4693-34.5758
580.57460.88860.25561.70340.49030.1412-0.18640.2513-0.1471-0.33620.1913-0.0148-0.09590.0528-0.00490.2778-0.08450.00560.4269-0.05030.2775-89.446-16.5873-31.1543
593.28341.6216-1.84886.68321.08791.722-0.03670.17760.1247-0.15140.03450.2745-0.0317-0.11040.00220.3163-0.051-0.07020.3040.10660.2659-94.6029-9.3202-27.5275
600.4352.26610.588511.99153.10580.8056-0.02090.0329-0.126-0.52970.1791-0.8269-0.1360.0379-0.15820.47280.08020.05290.46350.10990.5841-85.2297-1.6661-25.669
613.8306-4.2312-4.48318.18469.10116.5208-0.128-1.0653-1.2221.8401-1.02580.46290.670.57251.15380.4019-0.2204-0.0140.71020.41640.571-77.6671-32.190417.5144
620.7233-1.0644-1.14121.82770.60536.3297-0.07710.0471-0.00130.0763-0.0686-0.0290.14810.05740.14560.3439-0.04640.00570.2377-0.00460.318-77.6321-29.42492.6607
633.0717-0.87490.04361.95880.07182.83920.01240.002-0.1649-0.05540.00850.10050.20790.1913-0.0210.3576-0.00670.01840.23330.0060.2946-72.3059-28.1143-10.9741
640.20130.04620.07180.32370.1630.10350.0165-0.068-0.05260.0223-0.0281-0.00340.01340.0140.01160.34610.0010.0290.30570.02240.2925-74.858-23.251312.554
650.52730.0636-1.09421.5331-0.30822.2921-0.3689-0.0473-0.24650.1495-0.08220.53780.73360.11790.45110.4709-0.08140.14770.2227-0.02680.4132-90.8861-32.202919.7755
660.82760.6067-0.48291.3357-0.31720.2888-0.0714-0.09030.0494-0.07020.06170.00110.04060.06150.00980.3303-0.01320.02860.3003-0.0050.3009-73.1339-15.543711.1819
670.21590.0111-0.24480.213-0.16940.4007-0.0288-0.01570.0271-0.04140.0094-0.02460.0530.04370.01940.3191-0.00790.02560.3003-0.01550.3159-72.0274-17.50833.2737
680.82131.29130.38952.53250.37840.3155-0.05280.1013-0.0443-0.03860.1006-0.0362-0.0364-0.0011-0.04780.3111-0.02080.04730.2995-0.01770.3126-84.371-8.57899.8422
692.8549-1.45551.79310.9193-1.24561.9336-0.1368-0.0850.39190.04890.0139-0.0426-0.11710.05790.12290.3153-0.0297-0.00650.2101-0.02980.3862-70.287212.54391.8211
706.71110.4349-4.41930.42031.0657.7244-0.1519-0.16130.0993-0.16290.05760.0121-0.35620.19270.09440.3237-0.02670.03840.2426-0.03150.2825-70.020410.320119.1097
710.21090.5623-0.05881.7962-0.10580.02830.00250.05120.05520.05260.02870.03870.011-0.0055-0.03120.3129-0.01460.04150.3148-0.01180.3012-83.6641-9.358219.1496
720.85120.57660.69960.68430.20921.3377-0.1430.13560.195-0.02440.0720.2513-0.1696-0.04490.0710.262-0.01330.0740.287-0.0450.3315-93.9812-12.698823.13
731.209-0.3862-0.56250.43970.3770.3850.0198-0.118-0.07370.05310.0021-0.05630.02780.0367-0.02180.331-0.02630.01830.3343-0.00560.3234-68.2874-9.541525.9041
740.51360.3806-0.03191.89471.32231.13930.0433-0.0365-0.02550.0562-0.0426-0.0196-0.00050.0551-0.00080.3095-0.0230.02280.3237-0.00470.304-65.91020.414322.7025
750.88990.6912-0.93287.29062.74046.52950.193-0.35430.2444-0.2666-0.05890.4103-1.08510.1491-0.13410.3861-0.1210.09670.257-0.07150.2692-63.312512.95731.0327
761.2809-0.3027-0.2980.1529-0.08073.40660.1444-0.08950.0795-0.0372-0.0744-0.0619-0.07220.0845-0.07010.3121-0.06330.02620.3334-0.03090.3003-57.02575.039623.4264
775.828811.7028-1.746929.52793.99129.9450.3562-0.0726-0.11380.47860.1432-0.5841-0.25010.3093-0.49940.3332-0.0778-0.03260.3356-0.03160.2802-62.14891.381235.2555
782.65171.4026-0.33632.63820.25420.15550.1453-0.22070.04040.1701-0.11920.04590.05190.044-0.02610.3249-0.06480.04120.317-0.01440.2308-78.6303-8.076435.8223
796.90955.80830.35574.93480.27270.03270.1847-0.06190.0950.261-0.15940.1114-0.03080.0564-0.02540.3815-0.0640.08720.3118-0.03620.2454-90.9367-19.732331.8908
802.55730.4201-3.48637.49093.50296.9938-0.2607-0.5357-0.21870.04240.1673-0.40950.43220.8460.09340.2844-0.09860.03860.33940.08620.3429-76.4295-19.334729.8446
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 39
2X-RAY DIFFRACTION2A40 - 52
3X-RAY DIFFRACTION3A53 - 67
4X-RAY DIFFRACTION4A68 - 92
5X-RAY DIFFRACTION5A93 - 106
6X-RAY DIFFRACTION6A107 - 171
7X-RAY DIFFRACTION7A172 - 176
8X-RAY DIFFRACTION8A177 - 204
9X-RAY DIFFRACTION9A205 - 221
10X-RAY DIFFRACTION10A222 - 233
11X-RAY DIFFRACTION11A234 - 261
12X-RAY DIFFRACTION12A262 - 276
13X-RAY DIFFRACTION13A277 - 292
14X-RAY DIFFRACTION14A293 - 298
15X-RAY DIFFRACTION15A299 - 319
16X-RAY DIFFRACTION16A320 - 332
17X-RAY DIFFRACTION17A333 - 354
18X-RAY DIFFRACTION18A355 - 361
19X-RAY DIFFRACTION19A362 - 386
20X-RAY DIFFRACTION20A387 - 393
21X-RAY DIFFRACTION21B34 - 39
22X-RAY DIFFRACTION22B40 - 52
23X-RAY DIFFRACTION23B53 - 67
24X-RAY DIFFRACTION24B68 - 90
25X-RAY DIFFRACTION25B91 - 106
26X-RAY DIFFRACTION26B107 - 171
27X-RAY DIFFRACTION27B172 - 204
28X-RAY DIFFRACTION28B205 - 211
29X-RAY DIFFRACTION29B212 - 221
30X-RAY DIFFRACTION30B222 - 233
31X-RAY DIFFRACTION31B234 - 259
32X-RAY DIFFRACTION32B260 - 276
33X-RAY DIFFRACTION33B277 - 299
34X-RAY DIFFRACTION34B300 - 316
35X-RAY DIFFRACTION35B317 - 329
36X-RAY DIFFRACTION36B330 - 354
37X-RAY DIFFRACTION37B355 - 361
38X-RAY DIFFRACTION38B362 - 376
39X-RAY DIFFRACTION39B377 - 390
40X-RAY DIFFRACTION40B391 - 396
41X-RAY DIFFRACTION41C34 - 39
42X-RAY DIFFRACTION42C40 - 52
43X-RAY DIFFRACTION43C53 - 67
44X-RAY DIFFRACTION44C68 - 92
45X-RAY DIFFRACTION45C93 - 106
46X-RAY DIFFRACTION46C107 - 171
47X-RAY DIFFRACTION47C172 - 205
48X-RAY DIFFRACTION48C206 - 221
49X-RAY DIFFRACTION49C222 - 230
50X-RAY DIFFRACTION50C231 - 259
51X-RAY DIFFRACTION51C260 - 278
52X-RAY DIFFRACTION52C279 - 296
53X-RAY DIFFRACTION53C297 - 316
54X-RAY DIFFRACTION54C317 - 332
55X-RAY DIFFRACTION55C333 - 349
56X-RAY DIFFRACTION56C350 - 354
57X-RAY DIFFRACTION57C355 - 361
58X-RAY DIFFRACTION58C362 - 378
59X-RAY DIFFRACTION59C379 - 390
60X-RAY DIFFRACTION60C391 - 396
61X-RAY DIFFRACTION61D34 - 39
62X-RAY DIFFRACTION62D40 - 52
63X-RAY DIFFRACTION63D53 - 67
64X-RAY DIFFRACTION64D68 - 92
65X-RAY DIFFRACTION65D93 - 106
66X-RAY DIFFRACTION66D107 - 135
67X-RAY DIFFRACTION67D136 - 171
68X-RAY DIFFRACTION68D172 - 204
69X-RAY DIFFRACTION69D205 - 221
70X-RAY DIFFRACTION70D222 - 233
71X-RAY DIFFRACTION71D234 - 259
72X-RAY DIFFRACTION72D260 - 278
73X-RAY DIFFRACTION73D279 - 299
74X-RAY DIFFRACTION74D300 - 319
75X-RAY DIFFRACTION75D320 - 329
76X-RAY DIFFRACTION76D330 - 350
77X-RAY DIFFRACTION77D351 - 355
78X-RAY DIFFRACTION78D356 - 374
79X-RAY DIFFRACTION79D375 - 386
80X-RAY DIFFRACTION80D387 - 395

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://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