[日本語] English
- PDB-5mad: GFP-binding DARPin 3G61 -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 5mad
タイトルGFP-binding DARPin 3G61
要素
  • 3G61
  • Green fluorescent protein
キーワードFLUORESCENT PROTEIN / green fluorescent protein / designed ankyrin protein
機能・相同性
機能・相同性情報


bioluminescence / generation of precursor metabolites and energy
類似検索 - 分子機能
Ankyrin repeat-containing domain / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Beta Barrel ...Ankyrin repeat-containing domain / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Beta Barrel / Mainly Beta / Mainly Alpha
類似検索 - ドメイン・相同性
DI(HYDROXYETHYL)ETHER / Green fluorescent protein
類似検索 - 構成要素
生物種synthetic construct (人工物)
Aequorea victoria (オワンクラゲ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.53 Å
データ登録者Hansen, S. / Stueber, J. / Ernst, P. / Koch, A. / Bojar, D. / Batyuk, A. / Plueckthun, A.
引用ジャーナル: Sci Rep / : 2017
タイトル: Design and applications of a clamp for Green Fluorescent Protein with picomolar affinity.
著者: Hansen, S. / Stuber, J.C. / Ernst, P. / Koch, A. / Bojar, D. / Batyuk, A. / Pluckthun, A.
履歴
登録2016年11月3日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年12月6日Provider: repository / タイプ: Initial release
改定 2.02023年11月15日Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
カテゴリ: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id
改定 2.12024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

-
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

-
集合体

登録構造単位
A: 3G61
B: Green fluorescent protein
C: 3G61
D: Green fluorescent protein
E: 3G61
F: Green fluorescent protein
G: 3G61
H: Green fluorescent protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)178,75617
ポリマ-177,8848
非ポリマー8729
22,4471246
1
A: 3G61
B: Green fluorescent protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,7895
ポリマ-44,4712
非ポリマー3183
362
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
2
C: 3G61
D: Green fluorescent protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,7895
ポリマ-44,4712
非ポリマー3183
362
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
3
E: 3G61
F: Green fluorescent protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,6004
ポリマ-44,4712
非ポリマー1292
362
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
4
G: 3G61
H: Green fluorescent protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,5773
ポリマ-44,4712
非ポリマー1061
362
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)60.420, 83.070, 162.000
Angle α, β, γ (deg.)90.00, 94.59, 90.00
Int Tables number4
Space group name H-MP1211

-
要素

#1: タンパク質
3G61


分子量: 17017.029 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli K-12 (大腸菌)
#2: タンパク質
Green fluorescent protein


分子量: 27453.949 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Aequorea victoria (オワンクラゲ)
遺伝子: GFP / 発現宿主: Escherichia coli K-12 (大腸菌) / 参照: UniProt: P42212
#3: 化合物
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 8 / 由来タイプ: 合成 / : C4H10O3
#4: 化合物 ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 1 / 由来タイプ: 合成 / : Na
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1246 / 由来タイプ: 天然 / : H2O
Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.28 Å3/Da / 溶媒含有率: 45.98 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.1 M Sodium citrate tribasic, pH 5.5, 30% PEG 4000, 0.2 M Ammonium acetate

-
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: 1.00003 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2015年5月27日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.00003 Å / 相対比: 1
反射解像度: 1.53→48.76 Å / Num. obs: 237243 / % possible obs: 98.8 % / 冗長度: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Net I/σ(I): 15.79
反射 シェル解像度: 1.53→1.67 Å / 冗長度: 6.8 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 1.39 / CC1/2: 0.752

-
解析

ソフトウェア
名称バージョン分類
PHENIX(1.11_2567: ???)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 / 解像度: 1.53→48.76 Å / SU ML: 0.19 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 27.33 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.1987 11863 5.01 %
Rwork0.1706 --
obs0.172 236919 98.62 %
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: 1.53→48.76 Å
タンパク質核酸リガンド溶媒全体
原子数12068 0 57 1246 13371
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00612726
X-RAY DIFFRACTIONf_angle_d0.83817254
X-RAY DIFFRACTIONf_dihedral_angle_d15.0177512
X-RAY DIFFRACTIONf_chiral_restr0.0521909
X-RAY DIFFRACTIONf_plane_restr0.0052277
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5299-1.54730.38683910.37487482X-RAY DIFFRACTION99
1.5473-1.56550.40364190.35577514X-RAY DIFFRACTION99
1.5655-1.58460.34814020.34037483X-RAY DIFFRACTION99
1.5846-1.60470.35053890.33127542X-RAY DIFFRACTION99
1.6047-1.62580.34113810.31027541X-RAY DIFFRACTION99
1.6258-1.64810.31084170.29397417X-RAY DIFFRACTION99
1.6481-1.67160.32474340.28117368X-RAY DIFFRACTION98
1.6716-1.69660.30753780.27677096X-RAY DIFFRACTION94
1.6966-1.72310.29714110.25887343X-RAY DIFFRACTION97
1.7231-1.75130.27294100.23727511X-RAY DIFFRACTION100
1.7513-1.78150.26914140.22197534X-RAY DIFFRACTION99
1.7815-1.81390.26933800.21457529X-RAY DIFFRACTION99
1.8139-1.84880.22783840.20377600X-RAY DIFFRACTION100
1.8488-1.88660.23873870.2017606X-RAY DIFFRACTION100
1.8866-1.92760.22633870.19187525X-RAY DIFFRACTION100
1.9276-1.97240.22433890.18367561X-RAY DIFFRACTION99
1.9724-2.02180.23053790.18847592X-RAY DIFFRACTION99
2.0218-2.07640.21624280.18267479X-RAY DIFFRACTION99
2.0764-2.13750.20413540.1717271X-RAY DIFFRACTION95
2.1375-2.20650.20393980.1597412X-RAY DIFFRACTION98
2.2065-2.28540.19093970.1557570X-RAY DIFFRACTION99
2.2854-2.37690.19994090.15967573X-RAY DIFFRACTION100
2.3769-2.48510.20593990.15567574X-RAY DIFFRACTION100
2.4851-2.61610.1783800.1577620X-RAY DIFFRACTION100
2.6161-2.780.20243790.16237582X-RAY DIFFRACTION99
2.78-2.99460.17683950.17267483X-RAY DIFFRACTION98
2.9946-3.29590.19933550.17097435X-RAY DIFFRACTION97
3.2959-3.77260.18163870.15137678X-RAY DIFFRACTION99
3.7726-4.75250.14984300.12377534X-RAY DIFFRACTION99
4.7525-48.78450.16274000.15237601X-RAY DIFFRACTION97
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)
10.00080.0046-0.00320.0858-0.10020.10570.08810.4306-0.0759-0.1165-0.3606-0.2218-0.05830.3706-0.00010.37530.0075-0.04710.40640.00390.311959.9320.672245.7491
20.25990.10970.09390.41170.35240.7871-0.0181-0.0427-0.1962-0.05340.06610.0318-0.0315-0.4094-00.2913-0.0091-0.03580.35380.02110.296555.1099-0.01455.207
30.28680.14010.00490.61310.18520.78480.0584-0.3122-0.14650.1157-0.0830.02910.0067-0.54240.00010.2919-0.0168-0.00770.50610.09640.295554.3374-1.992473.1137
40.04010.0192-0.01760.04110.05410.08260.118-0.0530.02520.1648-0.2880.0835-0.1948-0.48460.00010.3775-0.0255-0.03680.55340.06170.274457.72544.300685.7822
50.36930.1427-0.3710.5380.13550.5529-0.1978-0.12050.18560.33640.3588-0.3665-0.6050.30270.51710.4846-0.02040.05310.1690.04730.337987.04519.815862.1996
60.5613-0.3765-0.62920.24110.39840.66950.03340.17920.0858-0.1177-0.0413-0.1877-0.04080.38380.00580.2858-0.00580.01870.24510.030.336190.0057-2.214758.1364
70.60360.35540.41380.2530.27460.3206-0.05480.19520.0587-0.18620.0548-0.0756-0.38860.0013-0.01720.41310.0264-0.00390.1350.05840.26373.252212.980358.3468
80.726-0.4024-0.29410.26250.3280.8283-0.1581-0.28710.0534-0.01350.2349-0.1563-0.04030.290.4610.3744-0.03130.0191-0.01390.0230.285880.73363.537268.7142
90.8057-0.0503-0.47770.3446-0.20470.4842-0.1402-0.25120.16130.12170.3683-0.2257-0.11950.49590.25430.3035-0.0674-0.00090.2225-0.02890.303589.31443.604368.356
100.57410.3523-0.26410.2518-0.06310.4058-0.23160.0589-0.3605-0.03020.12370.00540.22570.0047-0.26020.39170.07980.04240.13720.01490.382283.4716-15.567262.6932
110.1347-0.0425-0.05890.1178-0.05740.0671-0.1574-0.2524-0.1536-0.01220.14010.1884-0.03310.10790.00010.30790.0299-0.00790.20530.01330.259271.08045.750370.0275
120.1905-0.2753-0.07220.5280.05960.35-0.1499-0.1149-0.29940.05950.12380.30120.0089-0.13540.00270.2618-0.01540.00250.1166-0.00030.330274.467-1.983366.6195
130.5250.0765-0.15690.2924-0.25460.2435-0.2038-0.2563-0.4169-0.02590.2342-0.30740.0308-0.0322-0.10560.2737-0.04620.06430.04910.02710.382977.6137-9.174965.208
140.3104-0.03640.00590.2192-0.32160.47090.01110.05610.0957-0.12440.1292-0.18-0.2324-0.02450.02180.34710.00110.00760.1783-0.00060.323974.91177.652662.3104
150.0287-0.0419-0.00580.0947-0.01570.01130.06620.63420.0812-0.3196-0.2163-0.44460.20330.4782-0.00010.35310.05320.10690.4321-0.00360.388695.9614-7.945450.2668
160.16990.24660.06690.34440.05690.17370.05820.1848-0.0556-0.3238-0.01040.1034-0.2808-0.0505-00.43480.04820.01920.26340.02260.306671.83456.675754.8877
17-0.00030.01810.0170.09210.09260.0809-0.0146-0.65830.32630.2437-0.3140.0929-0.0107-0.2512-0.00010.36470.0682-0.04120.4236-0.09250.283482.62141.6301122.7064
180.0171-0.0227-0.02970.03310.09780.6766-0.0806-0.27970.04820.0890.10040.0204-0.08030.0751-0.00020.32260.0349-0.03560.2361-0.0030.260186.77411.4457117.92
190.4643-0.3123-0.32620.3335-0.06090.6940.01120.1167-0.0394-0.079-0.0334-0.07910.09870.34730.00220.28740.0291-0.01630.2210.01650.261988.3849-0.4385103.3394
200.0252-0.0164-0.00780.0185-0.01050.0146-0.05520.4274-0.0480.2157-0.02880.0932-0.37610.5431-0.00020.3348-0.04270.00350.3620.0390.233793.41935.021492.3667
210.05320.0910.04760.1390.05810.10650.285-0.00430.321-0.1948-0.206-0.01710.5314-0.0475-00.40170.04480.00450.2893-0.03740.288584.6417-6.112688.8837
220.0422-0.05030.02830.0569-0.04210.13710.06920.04730.0466-0.1342-0.2747-0.37280.02010.2170.00010.3590.0384-0.02350.32030.05420.316185.39493.978982.3726
230.5193-0.0936-0.37170.7154-0.32080.4568-0.07670.37150.60620.05640.27770.4481-0.3444-0.19910.13510.39680.06390.08880.31410.0880.523456.036810.646107.2696
240.65670.3393-0.75160.3025-0.40510.79160.0030.01980.2140.18060.12460.373-0.074-0.35720.01650.28210.04750.04310.28610.07360.380252.5798-1.2865110.2143
250.3682-0.0605-0.30050.2115-0.12290.38410.2484-0.02950.48420.36120.00040.2895-0.1663-0.03110.24210.37290.06950.08640.17740.05890.420566.368514.7803107.21
261.50310.472-0.57911.4687-0.5910.7072-0.26610.81810.2763-0.1360.5320.35830.1083-0.60420.35080.24920.0516-0.010.26960.19220.322956.29951.433599.245
270.3801-0.4437-0.06070.5647-0.01710.2509-0.2432-0.008-0.39830.17950.1681-0.0550.1799-0.0894-0.10870.3124-0.0740.08350.18840.01470.346358.997-14.8498105.929
280.14340.00040.00180.19130.14330.098-0.05240.29310.1130.06950.0826-0.0407-0.0906-0.244600.27370.0254-0.00780.22690.07040.266871.53356.282598.396
291.00630.0878-0.48260.05780.0330.2968-0.22810.2992-0.308-0.03080.27070.10010.1583-0.03280.05750.29850.0430.03580.13630.06680.305466.5023-4.435101.9111
300.25430.1509-0.03950.27060.14620.10490.01970.13550.29380.1920.19190.265-0.0763-0.1540.05560.31050.05070.02790.20540.10070.352167.70068.8977105.3745
310.3779-0.1081-0.11810.06880.08090.1141-0.0299-0.84950.17420.4245-0.03090.71110.4453-0.0094-0.00130.39830.01550.18290.41170.07260.501146.5836-6.9177118.1854
320.2219-0.19710.03560.2933-0.06940.0904-0.0471-0.30060.34330.34990.10530.0799-0.1114-0.0658-0.00280.37760.01510.03030.2011-0.00550.331770.74767.4451113.4096
330.0453-0.01230.05520.2703-0.3820.5687-0.03611.003-0.0895-0.0799-0.00760.2881-0.2846-0.4656-0.00920.38040.0595-0.03430.93050.04930.377269.529712.5571129.6335
340.7392-0.2718-0.11510.25720.15590.96020.06860.0269-0.07710.0715-0.0314-0.00590.1319-0.42220.0040.245-0.00520.00910.5324-0.03820.276972.559911.5005148.0854
350.1661-0.17450.00040.1541-0.030.27430.0143-0.12440.04230.03250.0619-0.02810.0406-0.0262-00.3159-0.00720.0080.5267-0.01820.319181.105811.6787165.3791
360.0014-0.00240.01350.0474-0.00580.0257-0.28430.02040.28380.2089-0.05950.0885-0.0211-0.2086-0.00030.47990.0669-0.00380.6659-0.0580.342974.983618.5918170.9982
370.0092-0.01080.01290.0125-0.01280.01270.07320.04260.25160.0011-0.15280.19390.15870.1171-0.00010.53-0.08360.21590.58340.08960.719197.716529.8694132.2576
380.57360.5534-0.15730.60760.09971.41180.2657-0.33830.29580.20590.37840.0056-0.04171.03480.74650.29250.0336-0.00160.7398-0.14750.3185110.636812.5036141.4991
390.02210.00810.02040.63470.49450.41520.10040.2704-0.00960.08370.4544-0.0246-0.15060.79440.49330.23890.07610.00230.752-0.07150.3581109.687811.2591137.0088
400.30820.1140.24710.04680.10310.2170.3383-0.0034-0.087-0.20850.18590.0104-0.29990.46440.19580.28890.01570.04970.5971-0.0390.3225101.460914.301130.5718
410.0623-0.01750.00020.00350.00250.0001-0.11860.22610.25680.14020.3306-0.31820.1680.57060.03770.30430.1805-0.06210.7497-0.19060.3871112.5081.3178140.0815
420.00480.0179-0.00240.0412-0.00550.0012-0.0411-0.20320.11880.10270.2056-0.21060.14440.45470.00020.2520.0612-0.03170.5121-0.10840.2914103.12116.557140.3744
430.0548-0.0525-0.09130.07580.12610.18710.24880.33140.5094-0.24180.0661-0.123-0.35710.123500.3924-0.01860.10810.3416-0.01690.486992.770625.8849139.4481
441.15650.0448-1.03470.8794-0.0761.3088-0.0216-0.72960.35370.01850.4022-0.19840.14110.93180.56950.2772-0.0207-0.02130.5874-0.17840.336104.684714.0228146.9711
450.32060.2908-0.16070.2687-0.14340.0738-0.2786-0.0756-0.25750.14680.1455-0.13940.23770.25150.00080.41890.2041-0.00510.4033-0.02230.3558101.2134-3.0474143.5279
460.0814-0.17030.12650.5503-0.52380.53550.0777-0.35230.1351-0.05840.0714-0.07130.05480.17810.10870.1963-0.0150.0380.4453-0.15210.331489.711418.7985150.4386
470.4377-0.0620.25430.116-0.19620.42250.0989-0.55210.01270.13550.00280.28580.18980.17210.17010.280.00860.02510.4125-0.08520.284792.396310.8501147.4642
480.50010.2075-0.52910.7108-0.24920.3872-0.0476-0.46550.0565-0.01320.20360.00860.00140.19030.29880.30830.00540.00690.3377-0.10610.263994.940914.1789147.9034
490.16470.23130.14370.584-0.10030.38930.06790.34260.1029-0.03330.0125-0.0405-0.0470.23230.05740.25680.0494-0.00160.514-0.08080.265597.24310.0842133.2179
500.12490.11780.05180.08880.03420.05450.1579-0.4919-0.27060.2424-0.15330.01410.3291-0.23430.00010.3934-0.0171-0.01810.5912-0.01350.3453117.70788.0774200.9356
510.05230.03970.01330.04220.01180.003-0.0936-0.2951-0.12350.08860.0758-0.1745-0.54120.37960.00010.3788-0.0095-0.05280.5041-0.08670.3965124.33215.6909199.2028
520.03720.0110.06470.2271-0.01250.0795-0.0879-0.4762-0.0930.05030.0761-0.05720.0150.063400.29730.0325-0.00460.35680.01070.312116.46845.2386194.4649
530.09240.08270.00730.0873-0.04630.0875-0.0071-0.26530.16160.1088-0.11570.0055-0.05110.364-00.2508-0.0132-0.01770.3636-0.02570.2887121.22914.4869188.9595
540.26310.0103-0.05470.202-0.08830.2030.02380.1688-0.0026-0.0905-0.01670.09890.05740.295200.26740.0281-0.0130.3061-0.03060.2727115.37829.1291182.7072
550.02490.0301-0.03570.0362-0.04460.0437-0.07810.5278-0.02840.2169-0.03560.00510.03460.54950.00010.2439-0.0024-0.01420.46570.00390.2925124.530615.8357179.4854
560.1046-0.0961-0.0820.2209-0.02910.2753-0.01440.4686-0.05870.10670.06310.02320.1686-0.034500.3020.0038-0.00680.5008-0.04550.3021113.69899.045173.9955
570.08360.09540.07960.1140.09230.0821-0.02860.5950.0850.10260.38610.0133-0.08440.58470.00780.2643-0.03680.01640.69220.02010.2708120.841318.0137169.2889
580.07280.0327-0.01410.0415-0.04210.0434-0.04530.4157-0.0565-0.04320.02080.13180.1441-0.12830.00340.3127-0.0155-0.01840.7594-0.07960.3327111.08487.6101166.0991
590.0251-0.03010.01430.0332-0.01890.02410.08880.48450.06350.14020.07620.4346-0.2079-0.266400.35440.03290.00860.79850.02220.3203107.10517.1348162.2373
600.0683-0.01250.03920.148-0.06080.1062-0.00430.35140.2554-0.0895-0.1854-0.32130.230.2413-0.04010.4318-0.02480.0160.92650.15310.3557115.128119.2176159.1443
610.02630.0420.03160.06590.04850.03030.2009-0.49140.4530.118-0.1573-0.1285-0.22720.05560.00020.4261-0.0119-0.01670.292-0.12320.405393.241429.8821197.4465
620.24410.1107-0.24060.1682-0.12870.2135-0.09870.08090.1369-0.07320.16840.1990.0172-0.2536-00.241-0.0362-0.01540.3559-0.03380.297779.859211.4618188.2722
630.1877-0.0758-0.090.405-0.31170.3268-0.0682-0.23670.1114-0.1120.09390.0511-0.1651-0.3268-00.2295-0.0363-0.01350.398-0.02390.285181.179610.9205193.8424
640.1852-0.1471-0.17340.09930.13980.14960.0408-0.4218-0.02080.09550.04630.02140.0297-0.137700.2680.0252-0.01610.421-0.04680.279689.47113.7412199.7416
650.011-0.01050.00530.00340.00110.0224-0.0161-0.2336-0.067-0.05410.2452-0.09280.3657-0.4906-0.00010.2793-0.0863-0.01250.35140.03520.331177.6630.5888189.3957
660.01980.0288-0.00350.0366-0.00510.0288-0.09610.01870.0058-0.13670.0120.2082-0.1289-0.125800.2355-0.0122-0.00120.2170.00180.252187.13245.8805189.3668
670.0455-0.04010.02110.1631-0.12170.0925-0.1047-0.29590.4509-0.03850.03080.0166-0.07170.0480.00010.2898-0.0087-0.01450.2727-0.0790.348100.955423.5515193.1897
680.85390.3086-0.16410.4423-0.49090.6047-0.1050.16370.2362-0.11670.13550.1416-0.1398-0.2480.00230.26040.019-0.02540.2496-0.01830.288886.953616.3948184.2237
690.3789-0.2023-0.22340.13130.05090.1967-0.24340.1517-0.2668-0.09980.11020.0060.24140.0092-0.05920.3747-0.08530.04720.1926-0.04290.346988.6719-4.0074185.5244
700.13060.0522-0.01650.16360.11660.0908-0.03770.27420.097-0.3190.09650.02540.3194-0.1753-00.2277-0.0085-0.01990.26990.04510.304100.622118.7021179.8894
710.501-0.0011-0.29510.07160.03560.1679-0.05130.25530.0189-0.0503-0.0591-0.1251-0.0572-0.064600.26910.00150.00010.22070.00470.308497.903410.5826182.5512
721.23360.641-0.47930.2921-0.26680.3821-0.07330.05670.0914-0.08880.0494-0.0579-0.04870.018300.26190.013-0.00590.1768-0.00750.243796.662312.9798185.4546
730.4243-0.38220.22880.47880.08810.55740.0576-0.36170.0430.0795-0.06-0.0046-0.0221-0.1696-00.2703-0.01920.00160.3395-0.00620.231190.12838.7384198.0788
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 147 )
4X-RAY DIFFRACTION4chain 'A' and (resid 148 through 165 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 24 )
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 64 )
7X-RAY DIFFRACTION7chain 'B' and (resid 68 through 81 )
8X-RAY DIFFRACTION8chain 'B' and (resid 82 through 104 )
9X-RAY DIFFRACTION9chain 'B' and (resid 105 through 128 )
10X-RAY DIFFRACTION10chain 'B' and (resid 129 through 147 )
11X-RAY DIFFRACTION11chain 'B' and (resid 148 through 158 )
12X-RAY DIFFRACTION12chain 'B' and (resid 159 through 170 )
13X-RAY DIFFRACTION13chain 'B' and (resid 171 through 187 )
14X-RAY DIFFRACTION14chain 'B' and (resid 188 through 208 )
15X-RAY DIFFRACTION15chain 'B' and (resid 209 through 218 )
16X-RAY DIFFRACTION16chain 'B' and (resid 219 through 233 )
17X-RAY DIFFRACTION17chain 'C' and (resid 12 through 24 )
18X-RAY DIFFRACTION18chain 'C' and (resid 25 through 58 )
19X-RAY DIFFRACTION19chain 'C' and (resid 59 through 124 )
20X-RAY DIFFRACTION20chain 'C' and (resid 125 through 133 )
21X-RAY DIFFRACTION21chain 'C' and (resid 134 through 147 )
22X-RAY DIFFRACTION22chain 'C' and (resid 148 through 166 )
23X-RAY DIFFRACTION23chain 'D' and (resid 0 through 24 )
24X-RAY DIFFRACTION24chain 'D' and (resid 25 through 64 )
25X-RAY DIFFRACTION25chain 'D' and (resid 68 through 91 )
26X-RAY DIFFRACTION26chain 'D' and (resid 92 through 128 )
27X-RAY DIFFRACTION27chain 'D' and (resid 129 through 147 )
28X-RAY DIFFRACTION28chain 'D' and (resid 148 through 158 )
29X-RAY DIFFRACTION29chain 'D' and (resid 159 through 187 )
30X-RAY DIFFRACTION30chain 'D' and (resid 188 through 208 )
31X-RAY DIFFRACTION31chain 'D' and (resid 209 through 218 )
32X-RAY DIFFRACTION32chain 'D' and (resid 219 through 233 )
33X-RAY DIFFRACTION33chain 'E' and (resid 9 through 35 )
34X-RAY DIFFRACTION34chain 'E' and (resid 36 through 133 )
35X-RAY DIFFRACTION35chain 'E' and (resid 134 through 157 )
36X-RAY DIFFRACTION36chain 'E' and (resid 158 through 168 )
37X-RAY DIFFRACTION37chain 'F' and (resid 4 through 11 )
38X-RAY DIFFRACTION38chain 'F' and (resid 12 through 24 )
39X-RAY DIFFRACTION39chain 'F' and (resid 25 through 36 )
40X-RAY DIFFRACTION40chain 'F' and (resid 37 through 48 )
41X-RAY DIFFRACTION41chain 'F' and (resid 49 through 56 )
42X-RAY DIFFRACTION42chain 'F' and (resid 57 through 64 )
43X-RAY DIFFRACTION43chain 'F' and (resid 68 through 91 )
44X-RAY DIFFRACTION44chain 'F' and (resid 92 through 128 )
45X-RAY DIFFRACTION45chain 'F' and (resid 129 through 147 )
46X-RAY DIFFRACTION46chain 'F' and (resid 148 through 158 )
47X-RAY DIFFRACTION47chain 'F' and (resid 159 through 170 )
48X-RAY DIFFRACTION48chain 'F' and (resid 171 through 198 )
49X-RAY DIFFRACTION49chain 'F' and (resid 199 through 231 )
50X-RAY DIFFRACTION50chain 'G' and (resid 9 through 23 )
51X-RAY DIFFRACTION51chain 'G' and (resid 24 through 35 )
52X-RAY DIFFRACTION52chain 'G' and (resid 36 through 49 )
53X-RAY DIFFRACTION53chain 'G' and (resid 50 through 67 )
54X-RAY DIFFRACTION54chain 'G' and (resid 68 through 91 )
55X-RAY DIFFRACTION55chain 'G' and (resid 92 through 100 )
56X-RAY DIFFRACTION56chain 'G' and (resid 101 through 124 )
57X-RAY DIFFRACTION57chain 'G' and (resid 125 through 133 )
58X-RAY DIFFRACTION58chain 'G' and (resid 134 through 147 )
59X-RAY DIFFRACTION59chain 'G' and (resid 148 through 157 )
60X-RAY DIFFRACTION60chain 'G' and (resid 158 through 168 )
61X-RAY DIFFRACTION61chain 'H' and (resid 2 through 11 )
62X-RAY DIFFRACTION62chain 'H' and (resid 12 through 24 )
63X-RAY DIFFRACTION63chain 'H' and (resid 25 through 36 )
64X-RAY DIFFRACTION64chain 'H' and (resid 37 through 48 )
65X-RAY DIFFRACTION65chain 'H' and (resid 49 through 56 )
66X-RAY DIFFRACTION66chain 'H' and (resid 57 through 64 )
67X-RAY DIFFRACTION67chain 'H' and (resid 68 through 81 )
68X-RAY DIFFRACTION68chain 'H' and (resid 82 through 128 )
69X-RAY DIFFRACTION69chain 'H' and (resid 129 through 147 )
70X-RAY DIFFRACTION70chain 'H' and (resid 148 through 158 )
71X-RAY DIFFRACTION71chain 'H' and (resid 159 through 170 )
72X-RAY DIFFRACTION72chain 'H' and (resid 171 through 208 )
73X-RAY DIFFRACTION73chain 'H' and (resid 209 through 232 )

+
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://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

+
2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月:コロナウイルスプロテーアーゼ

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか? / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

+
2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例:em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

-
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