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- PDB-5g4u: Association of three two-k-turn units based on Kt-7 3bU,3nU, form... -

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IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 5g4u
タイトルAssociation of three two-k-turn units based on Kt-7 3bU,3nU, forming a triangular-shaped structure
要素
  • 50S RIBOSOMAL PROTEIN L7AE
  • HMKT-7
キーワードRNA/PROTEIN / RNA-PROTEIN COMPLEX / RNA / KINK TURN / L7AE / NANO CRYSTAL PACKING / NANOTECHNOLOGY
機能・相同性
機能・相同性情報


ribonuclease P activity / tRNA 5'-leader removal / ribosome biogenesis / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cytoplasm
類似検索 - 分子機能
Ribosomal protein L7Ae, archaea / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like ...Ribosomal protein L7Ae, archaea / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
RNA / RNA (> 10) / Large ribosomal subunit protein eL8
類似検索 - 構成要素
生物種ARCHAEOGLOBUS FULGIDUS (古細菌)
HALOARCULA MARISMORTUI (好塩性)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.65 Å
データ登録者Huang, L. / Lilley, D.M.J.
引用ジャーナル: Nanoscale / 年: 2016
タイトル: A Quasi-Cyclic RNA Nano-Scale Molecular Object Constructed Using Kink Turns.
著者: Huang, L. / Lilley, D.M.J.
履歴
登録2016年5月17日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02016年9月28日Provider: repository / タイプ: Initial release
改定 1.12024年1月10日Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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: HMKT-7
B: HMKT-7
C: 50S RIBOSOMAL PROTEIN L7AE
D: 50S RIBOSOMAL PROTEIN L7AE
E: HMKT-7
F: HMKT-7
G: 50S RIBOSOMAL PROTEIN L7AE
H: 50S RIBOSOMAL PROTEIN L7AE
I: HMKT-7
J: HMKT-7
K: 50S RIBOSOMAL PROTEIN L7AE
L: 50S RIBOSOMAL PROTEIN L7AE


分子量 (理論値)分子数
合計 (水以外)118,16612
ポリマ－118,16612
非ポリマー00
水41423
1
E: HMKT-7
F: HMKT-7
G: 50S RIBOSOMAL PROTEIN L7AE
H: 50S RIBOSOMAL PROTEIN L7AE


分子量 (理論値)分子数
合計 (水以外)39,3894
ポリマ－39,3894
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-20.1 kcal/mol
Surface area17080 Å2
手法PISA
2
I: HMKT-7
J: HMKT-7
K: 50S RIBOSOMAL PROTEIN L7AE
L: 50S RIBOSOMAL PROTEIN L7AE


分子量 (理論値)分子数
合計 (水以外)39,3894
ポリマ－39,3894
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-23 kcal/mol
Surface area16900 Å2
手法PISA
3
A: HMKT-7
B: HMKT-7
C: 50S RIBOSOMAL PROTEIN L7AE
D: 50S RIBOSOMAL PROTEIN L7AE


分子量 (理論値)分子数
合計 (水以外)39,3894
ポリマ－39,3894
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-22.4 kcal/mol
Surface area17030 Å2
手法PISA
単位格子
Length a, b, c (Å)261.260, 69.220, 85.350
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
11
22
/ NCSアンサンブル:
ID
1
2

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要素

#1: RNA鎖
HMKT-7


分子量: 6171.753 Da / 分子数: 6 / 断片: KINK TURN MOTIF / 由来タイプ: 合成 / 由来: (合成) HALOARCULA MARISMORTUI (好塩性)
#2: タンパク質
50S RIBOSOMAL PROTEIN L7AE / RIBOSOMAL PROTEIN L8E


分子量: 13522.559 Da / 分子数: 6 / 断片: K-TURN BINDING DOMAIN, RESIDUES 2-119 / 由来タイプ: 組換発現 / 由来: (組換発現) ARCHAEOGLOBUS FULGIDUS (古細菌) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): GOLD PLYSS / 参照: UniProt: O29494
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 23 / 由来タイプ: 天然 / 式: 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: 2.99 Å3/Da / 溶媒含有率: 58.9 % / 解説: NONE
結晶化pH: 6.5 / 詳細: 1.6 M TRI-SODIUM CITRATE DIHYDRATE (PH 6.5)

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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: Diamond / ビームライン: I02 / 波長: 0.9191
検出器タイプ: DECTRIS PIXEL / 検出器: PIXEL / 日付: 2015年5月20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: 0.9191 Å / 相対比: 1
反射解像度: 2.65→52.25 Å / Num. obs: 45710 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / 冗長度: 5.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.6
反射 シェル解像度: 2.65→2.72 Å / 冗長度: 5.6 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1 / % 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
PHENIX(PHENIX.REFINE)精密化
xia2データ削減
xia2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 4BW0

4bw0


解像度: 2.65→51.87 Å / SU ML: 0.45 / σ(F): 1 / 位相誤差: 29.76
Rfactor反射数%反射
Rfree0.258 2261 4.9 %
Rwork0.229 --
obs0.23 45632 99.4 %
溶媒の処理減衰半径: 2 Å / VDWプローブ半径: 2 Å
精密化ステップサイクル: LAST / 解像度: 2.65→51.87 Å
タンパク質核酸リガンド溶媒全体
原子数5497 2454 0 23 7974
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0068364
X-RAY DIFFRACTIONf_angle_d1.12911860
X-RAY DIFFRACTIONf_dihedral_angle_d18.2094910
X-RAY DIFFRACTIONf_chiral_restr0.0621449
X-RAY DIFFRACTIONf_plane_restr0.0091094
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.70770.42591450.43692657X-RAY DIFFRACTION100
2.7077-2.77060.48481520.40952672X-RAY DIFFRACTION100
2.7706-2.83990.41731410.3652682X-RAY DIFFRACTION100
2.8399-2.91670.31921300.34052686X-RAY DIFFRACTION100
2.9167-3.00250.30961310.32212704X-RAY DIFFRACTION100
3.0025-3.09940.34041330.29942670X-RAY DIFFRACTION100
3.0994-3.21020.32331390.28122690X-RAY DIFFRACTION99
3.2102-3.33870.2951360.2752710X-RAY DIFFRACTION99
3.3387-3.49060.29621310.25282677X-RAY DIFFRACTION99
3.4906-3.67460.24141560.22032690X-RAY DIFFRACTION99
3.6746-3.90480.24861310.20732693X-RAY DIFFRACTION99
3.9048-4.20610.21741480.20042702X-RAY DIFFRACTION99
4.2061-4.62920.22051280.18942724X-RAY DIFFRACTION98
4.6292-5.29840.22251340.18352746X-RAY DIFFRACTION99
5.2984-6.67320.23961670.19882747X-RAY DIFFRACTION99
6.6732-51.87950.21061590.18532921X-RAY DIFFRACTION99
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)
10.9412-0.33970.10260.77170.17910.4419-0.06330.09770.0986-0.11080.13420.444-0.9827-0.20670.0020.6674-0.0209-0.15970.40280.15180.7432-15.2966-67.36721.283
22.38920.2511-1.77970.0623-0.18414.45060.7358-0.812-1.39990.48251.30171.7713-2.1959-1.5621.086-1.1617-0.4006-1.50130.8552-0.25821.0204-32.2237-80.7172-4.964
30.81170.8265-0.03990.79910.0110.3062-0.206-0.31150.93520.65960.2708-0.4966-0.9855-0.98850.00610.75470.171-0.09281.3180.02661.2487-37.4328-73.1861-5.0515
40.9487-0.33360.66290.4947-0.23370.9379-0.18250.2534-0.474-0.8490.27320.8689-0.0445-0.245-0.00050.5679-0.0204-0.17170.49470.06850.9117-15.2038-74.5189-3.9752
50.05220.0581-0.17260.2367-0.14650.4671.0361-1.4162-0.26951.1494-0.6832-0.10560.79460.33150.01790.56880.0042-0.10760.6014-0.0010.56430.2337-80.633121.769
60.51660.1402-0.16750.482-0.04380.0923-0.23640.4003-0.0761-0.11810.5150.1241-1.18510.6213-0.00050.5418-0.079-0.01380.4461-0.06880.57568.2335-72.02748.2629
70.76010.2241-0.4450.0618-0.07640.5688-0.46050.69060.915-0.3850.8674-0.4885-0.86770.54960.0090.569-0.1525-0.04420.5546-0.04530.6378-1.0036-77.1581-0.1337
80.3443-0.2899-0.14210.57610.15510.08660.50740.85770.3026-1.3931-0.3929-0.30760.56750.36770.00340.5607-0.0485-0.10820.4921-0.0490.5019-7.2185-84.07464.062
90.21520.3577-0.18681.9254-1.52951.4128-0.2580.1926-0.626-0.5771-0.01720.19970.92420.37660.02510.35910.06850.04150.4402-0.08410.50560.4964-83.13936.1221
100.1001-0.0783-0.02220.3764-0.01540.098-0.2376-0.03890.06170.04260.26130.46810.1922-0.10570.00060.5811-0.0282-0.04820.48470.06080.4144-10.2219-78.095716.8179
110.879-1.1994-1.20571.68171.64971.6492-0.0929-0.8028-1.1620.34070.9144-0.23971.36681.6566-0.0130.7003-0.0156-0.07160.4644-0.06710.5292-3.2844-89.300413.2281
120.7681-0.16950.0980.0808-0.07780.54070.0119-0.0821-0.177-0.5357-0.17210.21710.13260.594-0.03080.4301-0.0789-0.06230.3233-0.0740.4596-0.0809-76.248612.0238
130.0131-0.01260.12642.3495-0.71910.9695-0.091-0.14360.16550.191-0.0204-1.5041-0.74170.5159-0.0780.6615-0.1195-0.02890.5310.06490.3818-6.1421-68.25185.7533
140.46230.3410.03810.25480.05560.2293-0.2467-0.5398-0.4953-0.5806-0.0354-0.3018-0.11340.5815-0.0010.5254-0.16070.12360.5153-0.03120.47526.4663-79.43291.1691
150.8966-0.0708-0.66020.3270.21780.5144-0.3802-0.4956-1.5136-0.1398-0.1409-1.4430.40670.8883-0.01230.46420.0099-0.10960.4973-0.07110.848613.4511-82.568710.5166
160.18880.22050.13290.25840.08340.1479-0.5020.0365-0.6355-0.17210.3433-0.5806-0.09840.37910.00841.57060.1076-0.01862.0670.47171.3598-42.4529-76.3211-33.1547
170.247-0.11610.03710.1486-0.31.2089-0.4286-0.5560.1851-0.1606-1.3490.8421-0.5483-0.7748-0.05791.1064-0.1946-0.26021.52350.0831.4236-52.3314-85.2182-21.5077
180.2747-0.00510.23580.15920.1320.3260.1910.1609-0.20540.1840.40940.17050.3604-0.03390.02441.09450.14620.04941.36850.10791.499-41.2651-87.7939-14.529
190.2962-0.4514-0.05990.69350.08050.01260.78930.6432-0.097-0.45391.00840.38730.7320.8012-0.00091.09240.0263-0.38111.3992-0.02511.3065-32.8528-84.8625-18.8452
200.10380.0292-0.25790.0222-0.0280.52320.66560.01810.37260.8035-0.52420.00720.85360.1844-00.9324-0.2006-0.29831.3877-0.0081.1606-38.5694-87.4346-22.7102
210.12860.0962-0.04660.085-0.04190.0316-0.5870.4315-0.48090.01820.3687-0.20310.51510.1657-0.00211.27220.05040.0231.60730.34561.6556-36.0805-71.932-24.0846
22-0.0044-0.01080.0059-0.0001-0.00610.0153-0.20360.32-0.2346-0.0781-0.2210.00860.030.0765-0.0071.62250.20820.18542.04380.08641.4845-32.8286-83.8786-30.1974
230.1316-0.07830.0430.4434-0.42820.3213-0.40850.2006-0.6935-0.48960.48570.90890.13710.0042-0.00531.0573-0.1128-0.37051.53770.09881.4347-43.9419-80.0637-23.5175
240.11760.1339-0.24150.1513-0.2640.4875-0.13470.39820.75060.1768-0.7806-0.0867-0.69520.22320.00330.42490.07170.02171.60510.13661.6045-44.1859-76.2014-12.0313
250.090.00130.07250.00010.00560.06490.5741-0.1614-0.87230.16750.02760.39920.2467-0.8050.01180.9705-0.0954-0.05941.38610.09221.2446-44.723-92.5591-19.4996
260.06760.0790.06550.10630.06490.02630.24110.32810.53570.2054-0.1460.39140.04140.51910.00081.4586-0.0005-0.23641.6624-0.15791.2431-48.4598-92.0519-30.7325
270.0866-0.14140.02970.105-0.07060.02370.28411.3259-0.76230.2244-0.2305-0.0273-0.37741.3812-0.00010.84010.2624-0.04971.9558-0.10211.1292-48.7082-64.965914.0158
280.1649-0.1523-0.03680.28940.01360.01040.35920.243-0.26071.57430.46280.15890.32680.32990.00031.07690.01450.04021.2923-0.04771.2032-58.0838-59.54116.5146
290.01210.01970.00650.04570.12680.44550.3011-0.1853-0.50331.50771.0978-0.6841-0.79840.01630.00711.46380.02290.02781.45050.22311.3597-69.1514-45.662312.8569
300.04670.06760.03110.07710.0312-0.01780.1285-0.39730.01350.7288-0.47970.1753-1.1372-0.04340.00271.5237-0.3049-0.13291.64920.24431.1962-55.1259-36.164414.509
310.2720.1246-0.05210.0411-0.02730.0023-0.6495-0.174-1.00390.2170.42260.5921-0.99731.1834-0.0031.1874-0.4666-0.28071.5460.19431.0814-51.6685-36.97986.5196
320.1804-0.16820.10350.231-0.11150.0591-0.02210.19820.1117-0.4440.3657-0.4932-0.45490.08650.00041.3055-0.33310.05421.18410.03551.2388-60.7456-41.82710.3846
330.2966-0.06370.17860.1253-0.25720.39070.56840.6436-0.23150.0832-0.29660.0198-0.15560.38070.00231.02750.25270.06771.4810.07821.3959-62.1589-59.863115.0199
341.1645-0.06940.46430.0121-0.01340.20040.8754-0.12110.3484-0.16810.03710.35770.1725-0.53870.14962.15510.34140.36562.12040.4412.0524-53.6446-68.895942.9264
350.36370.10970.11130.08120.02010.025-0.6347-0.5156-0.37760.25481.06390.0639-0.1252-1.11060.0232.09090.06490.07192.01930.61011.8024-59.0518-81.297329.7525
360.48880.91530.08622.13120.54020.33420.01570.18-0.0526-0.2025-0.62090.05460.75070.2652-0.00661.13810.08210.01831.86530.06311.5373-65.8749-71.517923.2851
370.0003-0.0008-0.0054-0.0071-0.0004-0.01120.43950.0391-0.04880.4882-0.36060.37980.5939-0.81510.02551.53630.25820.39191.66180.2141.8134-66.5114-62.765128.6763
380.6463-0.26610.49350.1164-0.20590.31730.0660.0440.12170.5119-0.2552-0.51311.0035-0.05150.01951.98440.45640.29542.10690.66561.7471-66.5831-69.464732.1109
390.02670.1244-0.08090.7187-0.43090.25850.62610.24250.54730.35280.40620.874-0.7641-0.1567-0.09582.44010.44550.02692.29330.25461.4724-53.2301-60.940434.7095
400.5531-0.1748-0.12130.07580.14710.6518-0.3170.25220.0573-0.03630.2494-0.0325-0.1101-0.0575-0.0072.30230.46250.38282.93750.44122.3495-65.9665-63.820840.2604
410.13650.014-0.07840.07410.07250.1136-0.2493-1.0957-0.10830.7634-0.5576-0.25530.72730.2597-0.02631.75420.40760.17051.89860.40161.7366-58.056-72.406832.6225
420.10320.16340.17650.59370.77261.0578-0.684-0.5189-0.2398-0.20570.51810.20490.5798-0.2293-0.01551.50830.4744-0.07912.05390.24661.734-54.4452-69.923721.989
430.15750.1461-0.01940.2172-0.06680.0480.15350.42560.78880.05-0.7963-0.57810.4049-0.2261-0.00752.75460.88960.15992.10880.52172.015-69.0236-77.079527.6529
440.32110.3068-0.0380.38890.19310.3436-0.61530.78330.46220.49550.0333-1.0104-0.132-0.2105-0.04972.31420.4535-0.0021.81270.42751.7373-67.6532-81.024738.6716
450.58150.2789-0.3580.1376-0.17510.21880.7552-0.56690.62270.16670.4470.01570.28080.4512-0.0161.97140.4601-0.01051.943-0.25232.0015-73.5603-33.4344-13.9709
460.026-0.0349-0.07790.21340.04080.0749-0.47250.88571.6608-0.7248-0.4246-0.3156-0.119-0.2889-0.04982.97790.2660.61682.35990.30821.9413-68.804-20.8604-1.5672
470.0314-0.1012-0.08160.40040.31670.2437-0.1578-0.05940.5350.0639-0.2157-0.1143-0.3056-0.0166-0.01162.0189-0.08180.3751.4923-0.06871.3987-70.9621-29.85178.4716
480.1162-0.1075-0.04640.2368-0.1090.18950.1159-0.11040.0456-0.02520.27050.85170.1206-0.51810.01041.26790.24120.38021.67520.06161.6287-74.7214-38.67095.2376
490.4608-0.06-0.10670.0917-0.18480.4568-0.1709-0.67950.4399-0.8861-1.1162-0.44160.43060.3633-0.01412.11350.16420.0761.68370.31761.2663-76.9763-31.54392.1113
500.0147-0.08-0.05180.32620.12960.04840.34220.0609-0.4457-0.25550.41231.5575-0.34790.08690.04412.34310.5367-0.0221.63330.32171.2412-67.6091-41.0426-6.6279
510.0090.0074-0.01920.0172-0.02730.0399-0.27290.05760.38770.0814-0.61220.30030.038-0.0851-0.01892.29380.41160.2711.64130.43691.9303-80.5329-38.7771-4.3273
520.04740.07360.01770.1619-0.04390.04160.30470.99421.1066-0.2013-0.4260.4889-0.043-0.2128-0.0321.93940.27370.17731.82710.24811.4404-69.9586-30.6224-4.0067
530.00010.0052-0.00780.0015-0.00560.0098-0.2484-0.296-0.40370.01670.3022-0.2740.2385-0.0850.00841.70090.0530.11881.2602-0.08721.5012-60.5956-31.76723.1678
540.76470.52350.4990.33880.34990.33050.4631-0.94110.91980.2988-1.02910.57120.23260.03590.09431.9060.23790.041.29380.2362.0902-75.6284-24.38085.7523
55-0.016-0.0080.0023-0.0151-0.00930.0006-0.5415-0.63540.2254-0.2697-0.1741-0.8777-0.0770.72970.0382.40990.47970.09382.33060.2651.568-81.2038-20.6944-4.2233
560.1608-0.1585-0.05321.0021.04311.1859-0.3993-0.3733-0.8741-0.25271.33610.72581.8333-1.83620.09630.7834-0.5847-0.24641.16710.28410.9392-34.6277-33.859116.7464
570.66840.37691.01971.22841.6081.7848-0.1606-0.05630.0639-0.20090.40090.03880.6012-0.3260.00040.7515-0.0001-0.06960.53920.0810.5171-16.4724-31.74064.235
580.2615-0.242-0.16080.97840.11550.95150.289-0.1475-0.1407-0.08360.03980.13440.6806-0.22730.00030.8396-0.0033-0.08770.51180.08120.5603-16.2158-34.48120.9796
590.15090.0233-0.12270.0191-0.01050.069-0.54540.31960.5588-1.1-0.14051.17090.2562-0.53920.0110.7346-0.2866-0.22511.22190.13610.758-33.7361-27.184511.1631
600.0651-0.0413-0.04180.0889-0.06670.06830.319-0.70220.03140.3950.1062-0.03470.06630.2970.00480.47460.02410.07240.62990.09860.5522-16.3141-29.07640.397
610.24020.18540.20890.61920.27580.2783-0.143-0.55760.61030.148-0.13840.0723-0.4041-1.7649-0.01030.9840.41240.12450.88390.03160.5223-27.7671-16.652135.4998
620.3589-0.0589-0.14210.09770.15990.28360.21160.39470.3493-0.0076-0.12280.4215-0.9074-1.5573-0.03560.44620.16960.03080.51880.12350.6325-23.2717-16.824223.1198
630.3256-0.03430.10220.15020.06670.0783-0.51690.71520.8607-0.41940.20770.55580.67580.1237-0.01060.54820.0187-0.03850.53840.05370.6491-14.9741-23.243721.892
640.93470.9857-1.35850.9962-1.3641.81850.5270.11080.03370.803-0.3979-0.5319-1.051-0.24530.03730.46240.0964-0.02140.41870.09510.4178-16.2842-18.952728.3399
650.3586-0.32320.27720.3171-0.24380.20290.08180.4644-0.76210.4667-0.02070.17210.7644-0.31640.00050.51170.10550.02760.74490.05230.4924-18.6174-34.587729.9364
660.01860.086-0.02710.2213-0.07360.03070.22340.0341-0.1310.4809-0.1919-0.1739-0.11630.5332-0.00420.63020.0207-0.01210.48580.06650.3348-8.884-25.211931.2309
670.36-0.1187-0.53090.89340.32620.71660.1029-0.1199-0.18180.33330.06470.0625-0.3458-0.13790.00170.4272-0.0101-0.03110.55830.07440.4193-22.2326-24.214532.8996
680.02740.041-0.08820.1015-0.13750.2842-1.20020.63140.1939-1.19520.36690.28170.4798-1.5467-0.05490.6796-0.0307-0.20310.73520.00910.8244-30.2003-26.678424.3503
690.2243-0.3067-0.24181.40330.27180.4794-0.06570.30260.50720.00930.06870.1165-1.4953-0.30990.02050.79390.2328-0.02680.76910.23910.6188-21.1269-12.118828.5845
701.08760.4454-0.55350.5406-0.76241.02750.2656-0.93391.0661-0.31980.1147-0.6335-2.29520.19340.0561.48660.03870.05880.7104-0.01910.7217-16.9822-11.948639.6254
711.14691.50550.53922.01240.72480.2623-0.17361.4318-0.2559-0.22440.2648-0.5234-1.06350.2067-0.10960.6760.2847-0.02650.65970.05920.5083-21.7797-24.8886-28.2806
721.33231.26380.01351.35180.03950.0517-1.00321.6413-1.2521-0.44490.7136-0.55310.82081.7381-0.1490.91530.34490.16511.0022-0.0380.723-6.3064-33.5336-26.5619
730.642-0.63570.73231.7088-0.42240.92470.75160.60730.0457-0.5755-0.0832-0.20370.62840.62133.15910.9572-0.01470.15210.7581-0.04790.4273-5.136-29.6201-13.8964
740.05010.06560.11760.30510.4980.9203-0.040.31140.96481.1603-0.333-0.12190.0936-0.3146-0.10870.90560.1583-0.15010.4525-0.0370.7037-12.554-23.1097-10.7193
750.40150.18260.04110.49170.5810.8141-0.16830.60310.9481-0.1072-0.5067-0.2707-0.7556-0.7783-0.04040.6398-0.0233-0.12190.45040.13450.5808-9.4009-23.0305-17.9838
760.2563-0.10340.07780.2143-0.16230.1159-0.34430.2102-0.43080.0582-0.55881.5324-0.6465-1.1773-0.01880.74880.10250.04960.704-0.04260.7199-24.2121-28.0947-17.1166
771.021-0.41260.02880.1643-0.0044-0.0003-0.30410.12062.1427-0.19480.4158-0.1518-0.40460.34530.02481.0768-0.1921-0.06350.9730.04820.6997-17.1133-16.3835-18.9568
781.3093-0.3357-0.3520.1222-0.10940.78340.08740.44630.00440.1927-0.215-0.2741-0.48150.4468-0.00310.82350.0468-0.09670.57420.08430.4324-14.1412-29.5961-21.9664
790.27780.3003-0.13610.3453-0.13540.18710.3541-0.1977-0.41790.4978-0.35430.85791.069-0.08470.00170.76330.0404-0.0460.63550.03640.4962-13.3583-38.3903-14.0494
804.36380.17811.61523.48010.84331.18750.19870.9152-0.15830.5627-0.2943-1.72320.37791.21650.23690.70430.1329-0.17531.12570.1750.7712-1.8414-26.463-19.8876
810.19920.30240.21270.52910.36840.2171-0.3796-0.05610.8380.0211-0.0461-0.63870.3130.8858-0.03580.8756-0.06120.15271.12790.09760.8621-4.483-22.3164-30.5449
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 10 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 11 THROUGH 19 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 1 THROUGH 10 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 11 THROUGH 19 )
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 1 THROUGH 8 )
6X-RAY DIFFRACTION6CHAIN 'C' AND (RESID 9 THROUGH 25 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 26 THROUGH 31 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 32 THROUGH 40 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 41 THROUGH 50 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 51 THROUGH 61 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 62 THROUGH 68 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 69 THROUGH 86 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 87 THROUGH 93 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 94 THROUGH 103 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 104 THROUGH 117 )
16X-RAY DIFFRACTION16CHAIN 'D' AND (RESID 1 THROUGH 8 )
17X-RAY DIFFRACTION17CHAIN 'D' AND (RESID 9 THROUGH 25 )
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESID 26 THROUGH 31 )
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESID 32 THROUGH 40 )
20X-RAY DIFFRACTION20CHAIN 'D' AND (RESID 41 THROUGH 50 )
21X-RAY DIFFRACTION21CHAIN 'D' AND (RESID 51 THROUGH 61 )
22X-RAY DIFFRACTION22CHAIN 'D' AND (RESID 62 THROUGH 68 )
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 69 THROUGH 86 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 87 THROUGH 93 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 94 THROUGH 103 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 104 THROUGH 117 )
27X-RAY DIFFRACTION27CHAIN 'E' AND (RESID 1 THROUGH 5 )
28X-RAY DIFFRACTION28CHAIN 'E' AND (RESID 6 THROUGH 10 )
29X-RAY DIFFRACTION29CHAIN 'E' AND (RESID 11 THROUGH 15 )
30X-RAY DIFFRACTION30CHAIN 'E' AND (RESID 16 THROUGH 19 )
31X-RAY DIFFRACTION31CHAIN 'F' AND (RESID 1 THROUGH 5 )
32X-RAY DIFFRACTION32CHAIN 'F' AND (RESID 6 THROUGH 10 )
33X-RAY DIFFRACTION33CHAIN 'F' AND (RESID 11 THROUGH 19 )
34X-RAY DIFFRACTION34CHAIN 'G' AND (RESID 1 THROUGH 8 )
35X-RAY DIFFRACTION35CHAIN 'G' AND (RESID 9 THROUGH 25 )
36X-RAY DIFFRACTION36CHAIN 'G' AND (RESID 26 THROUGH 31 )
37X-RAY DIFFRACTION37CHAIN 'G' AND (RESID 32 THROUGH 40 )
38X-RAY DIFFRACTION38CHAIN 'G' AND (RESID 41 THROUGH 50 )
39X-RAY DIFFRACTION39CHAIN 'G' AND (RESID 51 THROUGH 61 )
40X-RAY DIFFRACTION40CHAIN 'G' AND (RESID 62 THROUGH 68 )
41X-RAY DIFFRACTION41CHAIN 'G' AND (RESID 69 THROUGH 86 )
42X-RAY DIFFRACTION42CHAIN 'G' AND (RESID 87 THROUGH 93 )
43X-RAY DIFFRACTION43CHAIN 'G' AND (RESID 94 THROUGH 103 )
44X-RAY DIFFRACTION44CHAIN 'G' AND (RESID 104 THROUGH 117 )
45X-RAY DIFFRACTION45CHAIN 'H' AND (RESID 1 THROUGH 8 )
46X-RAY DIFFRACTION46CHAIN 'H' AND (RESID 9 THROUGH 25 )
47X-RAY DIFFRACTION47CHAIN 'H' AND (RESID 26 THROUGH 31 )
48X-RAY DIFFRACTION48CHAIN 'H' AND (RESID 32 THROUGH 40 )
49X-RAY DIFFRACTION49CHAIN 'H' AND (RESID 41 THROUGH 50 )
50X-RAY DIFFRACTION50CHAIN 'H' AND (RESID 51 THROUGH 61 )
51X-RAY DIFFRACTION51CHAIN 'H' AND (RESID 62 THROUGH 68 )
52X-RAY DIFFRACTION52CHAIN 'H' AND (RESID 69 THROUGH 86 )
53X-RAY DIFFRACTION53CHAIN 'H' AND (RESID 87 THROUGH 93 )
54X-RAY DIFFRACTION54CHAIN 'H' AND (RESID 94 THROUGH 103 )
55X-RAY DIFFRACTION55CHAIN 'H' AND (RESID 104 THROUGH 117 )
56X-RAY DIFFRACTION56CHAIN 'I' AND (RESID 1 THROUGH 5 )
57X-RAY DIFFRACTION57CHAIN 'I' AND (RESID 6 THROUGH 19 )
58X-RAY DIFFRACTION58CHAIN 'J' AND (RESID 1 THROUGH 15 )
59X-RAY DIFFRACTION59CHAIN 'J' AND (RESID 16 THROUGH 19 )
60X-RAY DIFFRACTION60CHAIN 'K' AND (RESID 1 THROUGH 8 )
61X-RAY DIFFRACTION61CHAIN 'K' AND (RESID 9 THROUGH 25 )
62X-RAY DIFFRACTION62CHAIN 'K' AND (RESID 26 THROUGH 31 )
63X-RAY DIFFRACTION63CHAIN 'K' AND (RESID 32 THROUGH 40 )
64X-RAY DIFFRACTION64CHAIN 'K' AND (RESID 41 THROUGH 50 )
65X-RAY DIFFRACTION65CHAIN 'K' AND (RESID 51 THROUGH 61 )
66X-RAY DIFFRACTION66CHAIN 'K' AND (RESID 62 THROUGH 68 )
67X-RAY DIFFRACTION67CHAIN 'K' AND (RESID 69 THROUGH 86 )
68X-RAY DIFFRACTION68CHAIN 'K' AND (RESID 87 THROUGH 93 )
69X-RAY DIFFRACTION69CHAIN 'K' AND (RESID 94 THROUGH 103 )
70X-RAY DIFFRACTION70CHAIN 'K' AND (RESID 104 THROUGH 117 )
71X-RAY DIFFRACTION71CHAIN 'L' AND (RESID 1 THROUGH 8 )
72X-RAY DIFFRACTION72CHAIN 'L' AND (RESID 9 THROUGH 25 )
73X-RAY DIFFRACTION73CHAIN 'L' AND (RESID 26 THROUGH 31 )
74X-RAY DIFFRACTION74CHAIN 'L' AND (RESID 32 THROUGH 40 )
75X-RAY DIFFRACTION75CHAIN 'L' AND (RESID 41 THROUGH 50 )
76X-RAY DIFFRACTION76CHAIN 'L' AND (RESID 51 THROUGH 61 )
77X-RAY DIFFRACTION77CHAIN 'L' AND (RESID 62 THROUGH 68 )
78X-RAY DIFFRACTION78CHAIN 'L' AND (RESID 69 THROUGH 86 )
79X-RAY DIFFRACTION79CHAIN 'L' AND (RESID 87 THROUGH 93 )
80X-RAY DIFFRACTION80CHAIN 'L' AND (RESID 94 THROUGH 103 )
81X-RAY DIFFRACTION81CHAIN 'L' AND (RESID 104 THROUGH 117 )

+
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

他の情報も見る