[日本語] English
- PDB-4pib: Crystal Structure of Uncharacterized Conserved Protein PixA from ... -

+
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: 4pib
タイトルCrystal Structure of Uncharacterized Conserved Protein PixA from Burkholderia thailandensis
要素inclusion body protein
キーワードUNKNOWN FUNCTION / beta-fold / inclusion body protein / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
機能・相同性Inclusion body protein / Uncharacterised protein family PixA/AidA / PixA-like superfamily / Inclusion body protein / Immunoglobulin-like / Sandwich / Mainly Beta / metal ion binding / Uncharacterized protein
機能・相同性情報
生物種Burkholderia thailandensis (バクテリア)
手法X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 2 Å
データ登録者Kim, Y. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
引用ジャーナル: To Be Published
タイトル: Crystal Structure of Uncharacterized Conserved Protein PixA from Burkholderia thailandensis
著者: Kim, Y. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
履歴
登録2014年5月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年7月2日Provider: repository / タイプ: Initial release
改定 1.12017年11月22日Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
カテゴリ: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
改定 1.22023年12月27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_struct_conn_angle / refine_hist / 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_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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.ptnr3_symmetry / _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.pdbx_ptnr2_label_alt_id / _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.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_label_seq_id / _struct_conn.ptnr2_symmetry

-
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: inclusion body protein
B: inclusion body protein
C: inclusion body protein
D: inclusion body protein
E: inclusion body protein
F: inclusion body protein
G: inclusion body protein
H: inclusion body protein
I: inclusion body protein
J: inclusion body protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)211,20059
ポリマ-208,75710
非ポリマー2,44449
15,331851
1
A: inclusion body protein
B: inclusion body protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)42,49315
ポリマ-41,7512
非ポリマー74213
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-67 kcal/mol
Surface area14120 Å2
手法PISA
2
C: inclusion body protein
D: inclusion body protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)42,31413
ポリマ-41,7512
非ポリマー56211
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-68 kcal/mol
Surface area14290 Å2
手法PISA
3
E: inclusion body protein
F: inclusion body protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)42,10311
ポリマ-41,7512
非ポリマー3519
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-91 kcal/mol
Surface area14160 Å2
手法PISA
4
G: inclusion body protein
H: inclusion body protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)42,21111
ポリマ-41,7512
非ポリマー4609
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-72 kcal/mol
Surface area14200 Å2
手法PISA
5
I: inclusion body protein
J: inclusion body protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)42,0799
ポリマ-41,7512
非ポリマー3287
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-84 kcal/mol
Surface area13860 Å2
手法PISA
単位格子
Length a, b, c (Å)79.806, 84.868, 249.693
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDモデル要素
11D-305-

HOH

-
要素

-
タンパク質 , 1種, 10分子 ABCDEFGHIJ

#1: タンパク質
inclusion body protein


分子量: 20875.650 Da / 分子数: 10 / 由来タイプ: 組換発現
由来: (組換発現) Burkholderia thailandensis (バクテリア)
: E264 / 遺伝子: BTH_I2413 / プラスミド: pMCSG68 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)gold / 参照: UniProt: Q2SVW5

-
非ポリマー , 5種, 900分子

#2: 化合物...
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 31 / 由来タイプ: 合成 / : Ca
#3: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 7 / 由来タイプ: 合成 / : Cl
#4: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 9 / 由来タイプ: 合成 / : C3H8O3
#5: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 2 / 由来タイプ: 合成 / : C2H6O2
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 851 / 由来タイプ: 天然 / : H2O

-
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: 2.04 Å3/Da / 溶媒含有率: 39.68 %
結晶化温度: 289 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5
詳細: 0.2 M calcium chloride, 0.1 M HEPES pH 8.5, 20 %(w/v) PEG4000

-
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: APS / ビームライン: 19-ID / 波長: 0.97901 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2013年3月13日
放射モノクロメーター: double crystal monochromator / 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: 0.97901 Å / 相対比: 1
反射解像度: 2→50 Å / Num. obs: 114270 / % possible obs: 99.7 % / 冗長度: 6.1 % / Rsym value: 0.086 / Net I/av σ(I): 17.7 / Net I/σ(I): 8.2
反射 シェル解像度: 2→2.3 Å / 冗長度: 5.8 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.562 / % possible all: 99.6

-
解析

ソフトウェア
名称バージョン分類
PHENIX(phenix.refine: dev_1621)精密化
HKL-3000位相決定
RESOLVEモデル構築
PHENIX位相決定
HKL-3000データスケーリング
精密化構造決定の手法: 単波長異常分散 / 解像度: 2→36.111 Å / SU ML: 0.21 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 23.15 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.224 5263 5.05 %random
Rwork0.181 ---
obs0.183 104282 90.94 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 2→36.111 Å
タンパク質核酸リガンド溶媒全体
原子数13309 0 100 851 14260
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00713933
X-RAY DIFFRACTIONf_angle_d1.21919044
X-RAY DIFFRACTIONf_dihedral_angle_d14.164864
X-RAY DIFFRACTIONf_chiral_restr0.0492138
X-RAY DIFFRACTIONf_plane_restr0.0062490
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02680.2705840.19711644X-RAY DIFFRACTION46
2.0268-2.05060.2561090.20711800X-RAY DIFFRACTION51
2.0506-2.07560.241940.20942019X-RAY DIFFRACTION56
2.0756-2.10190.25861330.21192219X-RAY DIFFRACTION62
2.1019-2.12960.23951350.20792508X-RAY DIFFRACTION70
2.1296-2.15870.29881510.20972854X-RAY DIFFRACTION79
2.1587-2.18960.2411800.20833026X-RAY DIFFRACTION86
2.1896-2.22220.27012030.20663293X-RAY DIFFRACTION92
2.2222-2.2570.28061860.19863452X-RAY DIFFRACTION96
2.257-2.29390.24271700.20473585X-RAY DIFFRACTION98
2.2939-2.33350.24391890.19683548X-RAY DIFFRACTION99
2.3335-2.37590.23971960.20343590X-RAY DIFFRACTION99
2.3759-2.42160.25751950.2043593X-RAY DIFFRACTION100
2.4216-2.4710.26781960.20443553X-RAY DIFFRACTION100
2.471-2.52470.28531890.21493588X-RAY DIFFRACTION100
2.5247-2.58350.28461720.19943658X-RAY DIFFRACTION100
2.5835-2.6480.24612050.19683580X-RAY DIFFRACTION100
2.648-2.71960.24642000.20363576X-RAY DIFFRACTION100
2.7196-2.79960.23812040.20483576X-RAY DIFFRACTION100
2.7996-2.88990.25851930.20133605X-RAY DIFFRACTION100
2.8899-2.99320.2571840.19843646X-RAY DIFFRACTION100
2.9932-3.1130.2141720.19953628X-RAY DIFFRACTION100
3.113-3.25460.22841920.18753648X-RAY DIFFRACTION100
3.2546-3.4260.22041790.1833653X-RAY DIFFRACTION100
3.426-3.64050.20781820.16653660X-RAY DIFFRACTION100
3.6405-3.92130.20672110.15913625X-RAY DIFFRACTION100
3.9213-4.31530.15961930.14153673X-RAY DIFFRACTION100
4.3153-4.93840.16791670.12763726X-RAY DIFFRACTION100
4.9384-6.21670.18621820.16483767X-RAY DIFFRACTION100
6.2167-36.11650.21252170.18413726X-RAY DIFFRACTION95
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)
12.38090.95870.15965.7173-1.34693.38920.0793-0.11580.21080.4232-0.04020.3938-0.1707-0.4164-0.10430.2471-0.06030.00530.3233-0.08110.163313.902718.535520.3865
22.6290.996-0.40121.0096-0.4762.0942-0.0986-0.06380.6076-0.1307-0.06170.4807-0.6734-0.58530.4610.7277-0.15510.02060.554-0.25230.499915.481433.077928.9732
31.75040.16571.27380.22810.26522.46470.2109-0.5369-0.03450.3137-0.10160.38650.3288-0.7133-0.04180.2736-0.16030.0660.5101-0.06730.27689.707813.502520.7814
42.81081.2019-0.93082.2570.21070.67140.1807-0.05-0.30660.1124-0.0410.44020.6958-0.6951-0.17590.5338-0.34420.00090.56680.01530.31819.38536.384424.9202
50.87190.0189-0.20760.5129-0.21071.35420.1658-0.45430.05730.2364-0.2220.049-0.0155-0.10230.00720.2208-0.15240.02190.3956-0.03170.188318.510917.167925.0923
61.2833-0.2365-2.54550.79040.81965.22590.3009-0.0369-0.28050.30670.1188-0.28060.33340.6657-0.30180.25540.056-0.06940.5671-0.03030.290632.63611.416719.2422
71.5810.09950.52511.17970.72750.58280.33570.4032-0.0626-0.0127-0.0087-0.02390.35780.1662-0.29180.1960.0008-0.02340.516-0.06170.244628.870712.056412.4817
82.7742.6189-0.92542.4747-0.87470.30590.0802-0.302-0.27040.16910.02150.6120.2312-0.37380.15380.0996-0.64440.28420.6888-0.04850.3856.619910.970334.1522
92.47430.2701-0.15292.216-0.02581.94650.1273-0.1290.29230.0279-0.13460.1855-0.1108-0.24830.02460.2281-0.11580.01620.297-0.0590.184318.562424.120622.4309
102.80570.2807-0.15331.87280.0492.59340.09190.2259-0.502-0.0582-0.07740.22290.4821-0.1020.06450.24350.0212-0.05510.2957-0.09930.238615.57737.664.4589
113.6419-0.38160.81671.02231.60834.5149-0.0935-0.4755-1.14890.22460.11470.63180.5489-0.4805-0.10630.21430.01730.01460.52380.00340.4973.615614.56066.7444
121.33620.1530.07621.01110.15222.58840.05840.35740.0376-0.00970.0059-0.04620.00240.0945-0.08960.12210.0192-0.00720.3267-0.04320.184917.568215.32851.271
130.87180.63731.79971.89363.02025.76130.02180.66260.2276-0.43950.1697-0.0435-0.66790.52-0.1240.2441-0.12680.03310.5675-0.01980.3330.886823.54289.5647
141.43720.66990.17721.20140.97621.13540.2764-0.3113-0.07040.1852-0.1068-0.1136-0.06690.0632-0.16280.197-0.0660.0190.48-0.03280.199326.994821.200115.0669
152.1185-0.87780.86252.1244-0.1080.69460.09470.2774-0.41660.10040.08050.30040.1426-0.3255-0.25620.13150.1105-0.03850.5961-0.10260.270913.622810.5473-2.538
162.17860.23240.24791.61330.56582.09110.1043-0.1463-0.26920.10520.0504-0.1870.45760.1482-0.12850.28760.1024-0.0660.3891-0.09920.320722.01546.38935.748
171.90760.8145-0.02360.65250.78822.6708-0.16740.41210.3633-0.37310.03280.1473-0.64390.36430.07740.3419-0.1803-0.05420.3150.04990.255112.354722.266853.969
183.87631.75131.29190.78790.56573.3484-0.1120.23240.8928-0.1318-0.25840.2571-0.5463-0.2220.21860.3231-0.1660.06150.6816-0.05410.575228.797921.157357.9344
190.94950.1351-0.24560.55860.21041.245-0.35530.3420.1604-0.1450.2567-0.0363-0.05620.6051-0.02750.1937-0.19070.01990.4210.00950.180818.205115.123651.1129
201.720.92730.74421.9012-0.36640.7018-0.1050.1632-0.2219-0.02920.0258-0.03870.15290.10530.10520.1369-0.00190.01880.128-0.03220.221311.79912.837763.2757
212.6616-0.2361-0.34880.98060.28741.067-0.09610.29860.3145-0.16010.0789-0.003-0.2370.3965-0.01760.2437-0.1515-0.03130.28860.04090.205711.888619.306951.3485
223.7327-1.2325-1.02672.92590.5953.3062-0.14780.01830.25840.00160.08050.1016-0.19850.25380.06960.2143-0.0828-0.01990.11890.01630.167313.13221.551271.3117
231.714-1.38511.04122.4547-0.42161.6063-0.1584-0.569-0.10670.07970.0962-0.69990.49511.25670.06350.27050.18790.12150.88950.04760.359931.55435.461269.5605
241.7478-1.24640.64293.75270.71570.9126-0.237-0.1393-0.38160.48450.1328-0.77390.41660.94470.12580.33710.1217-0.12690.50280.04620.441128.20294.163279.4434
251.7039-0.95010.02993.56210.72092.2973-0.13310.05620.1310.01030.07-0.2672-0.1850.6833-0.16250.2706-0.3236-0.07720.3229-0.00360.153522.376320.192369.0104
260.09650.65670.03244.5354-0.26695.684-0.30960.10480.0422-0.64740.0512-0.88490.00441.14770.22590.387-0.13650.09830.38550.04680.453420.77829.075968.9604
270.8810.69460.80011.10860.38681.58920.0170.16840.0584-0.156-0.0148-0.2188-0.15420.6952-0.16960.1366-0.15430.01810.15060.00910.199116.01119.020270.7327
280.67780.1703-0.32781.4601-0.22160.24330.0755-0.17390.03220.2871-0.14980.02040.06640.11780.08480.1398-0.0568-0.01360.1279-0.01340.160115.774116.116382.2317
293.3802-0.19394.09340.2654-0.53427.8488-0.2013-0.40450.4584-0.10080.04470.0325-0.1247-0.37340.13440.1468-0.02460.00640.1226-0.04870.20651.41868.342967.5899
301.71580.93190.89391.72410.08730.6124-0.03160.2335-0.1446-0.20160.0859-0.0746-0.01810.1351-0.03030.1351-0.02520.01910.1118-0.00370.1965.298210.426962.1442
312.0227-0.30930.06055.38250.89280.820.0541-0.01330.15170.26560.0209-0.4788-0.14570.2896-0.11440.1495-0.05010.00440.1470.01760.148821.205517.19579.5522
322.115-0.13090.43650.9226-1.00541.7770.10880.2281-0.36950.02340.0458-0.5180.27290.5966-0.14940.14350.02490.02350.2326-0.04170.183420.51177.489271.942
331.9973-0.1349-0.31312.16920.34072.3685-0.1-0.1343-0.20830.2965-0.04090.42690.0737-0.35660.14890.2936-0.0240.0650.18010.0070.22418.108115.1448122.3456
340.932-1.3589-1.07732.84420.44612.66350.18870.1713-0.7703-0.2824-0.27150.56520.469-0.26230.07020.39430.034-0.07380.1971-0.07710.435920.02183.6173118.6521
350.4927-0.31770.32870.8995-0.30171.74480.0303-0.0014-0.05730.3561-0.05180.03780.05310.03270.00230.2956-0.02790.01040.11590.01080.181417.097515.5726125.1945
361.76682.1113-2.36443.0113-3.08923.44780.182-0.20430.08860.4833-0.1679-0.2918-0.47150.5564-0.00530.3595-0.05890.01340.2034-0.03750.296523.496931.5034117.5121
370.97460.0421-0.47271.8043-0.04240.41970.10280.17090.0798-0.09490.0123-0.0252-0.30240.0417-0.10260.3161-0.0330.01910.1356-0.00750.199621.665327.3978111.8836
382.6527-1.55650.61432.1967-0.7390.81370.0477-0.06-0.50790.24910.03620.42870.2655-0.0809-0.09050.3904-0.00490.05440.1485-0.00790.26612.19113.7079128.3652
391.63540.2844-0.8541.18210.52271.6108-0.0257-0.0288-0.01750.17260.1310.448-0.2458-0.498-0.05020.2997-0.00210.03840.1998-0.03620.23867.51420.9143121.1
402.39970.1952-0.41582.6622-0.63922.8321-0.1140.1652-0.2665-0.0248-0.044-0.3490.27480.30350.13720.2292-0.01270.03230.2212-0.02640.203223.594413.5833104.0021
410.70480.22570.24051.03170.45961.84470.0306-0.0339-0.16230.0932-0.02930.02270.3265-0.1834-0.00480.2396-0.05290.00740.14570.00220.183113.792914.1286102.2038
420.32620.1972-0.28971.80880.18160.3563-0.0408-0.04940.13490.0448-0.05980.1266-0.4388-0.18750.05680.35070.01220.01690.1307-0.00180.238312.092929.9365112.612
431.9215-0.10820.12541.4104-0.16381.7559-0.02010.0631-0.09980.0850.0614-0.07420.30220.3123-0.00020.2239-0.03550.04430.14950.02320.181922.414716.3607101.9534
441.9798-0.13940.66531.72030.4211.7149-0.105-0.11590.0344-0.35680.09820.2656-0.2192-0.16850.00070.25330.013-0.060.1240.02050.24217.974614.8335154.267
450.47120.27391.57094.26140.55615.24160.06040.38060.84670.02730.08170.5249-0.441-0.6076-0.13410.39740.0219-0.02210.23840.01880.546516.507830.3752157.5171
460.8669-0.15570.21681.6515-0.51191.3325-0.02520.03120.0649-0.25610.0175-0.0127-0.3129-0.0271-0.01820.2822-0.015-0.02690.0865-0.00490.180316.443818.1618151.3062
471.65-0.17740.23631.44460.35191.035-0.0371-0.0764-0.0184-0.23550.05910.0671-0.11730.0468-0.0370.1918-0.0113-0.00380.0781-0.00530.160417.853410.9169156.4037
484.32671.5075-0.20363.7476-0.45362.0792-0.1963-0.62880.05570.08070.01560.1415-0.034-0.21110.12240.19410.0582-0.04140.2871-0.03210.175210.384715.4788171.5468
495.53315.30183.88585.19843.43243.461-0.50060.35820.86760.23290.0034-0.9388-1.05360.65480.27330.4234-0.0795-0.21790.35880.0710.597532.043826.6887167.9833
502.3813-3.36452.35756.0961-1.69816.1381-0.18490.13030.43190.2512-0.3002-0.7475-0.58290.59480.17660.3249-0.0476-0.17330.2214-0.04040.360233.095122.8657177.9332
516.352.554-1.69642.9993-1.04153.45140.0282-0.12010.67130.29440.13630.0067-0.57150.0064-0.12460.27180.0387-0.06530.162-0.06160.28214.904423.5262169.0738
525.9059-1.12980.94140.7841.23443.98420.028-0.20490.99330.11660.12360.218-0.4928-0.1302-0.16910.27550.1497-0.01110.3389-0.06320.36286.044724.0929170.9717
531.3895-0.3249-0.11461.47650.15970.9269-0.196-0.43720.1210.21670.1671-0.0001-0.2629-0.2664-0.03940.1760.0849-0.01710.3277-0.03410.153916.536115.3776175.6215
541.16421.35571.67193.26570.61973.4646-0.1409-0.3134-0.05030.24250.0459-0.02030.25460.05940.14140.15110.0804-0.01890.14440.0160.182618.2137-0.0063167.3856
551.6168-0.27660.5481.93040.05080.20140.0025-0.0865-0.0347-0.15390.14640.00050.14630.0102-0.11790.15770.0054-0.01850.09720.02110.171717.62914.4003161.7574
563.7621-0.4369-1.19231.02730.06670.4095-0.0375-0.21960.54060.17360.0863-0.0519-0.4637-0.362-0.18470.2560.1501-0.05560.3993-0.12620.249418.52920.7065178.5072
572.09880.00160.62141.76090.08991.4445-0.1138-0.14050.44360.07580.1629-0.2626-0.25440.1212-0.02490.20540.0143-0.05910.1989-0.0260.256726.206917.4878170.865
582.2562-0.7915-0.05372.0512-0.00523.23310.2673-0.3998-0.71130.104-0.2528-0.05720.48710.4198-0.04190.23720.008-0.06060.27840.06350.309615.97177.1053222.1687
593.11452.4753-0.55452.6433-1.38561.4314-0.2260.1691-0.3262-0.3870.2472-0.64430.23520.5141-0.06220.255-0.05490.04980.73050.01260.462131.0114.8281218.278
601.401-1.01430.15320.7443-0.30861.3457-0.0626-0.17140.0690.01620.1337-0.1235-0.15420.5345-0.09310.1261-0.0294-0.01490.3486-0.01860.202218.756515.6183225.3865
611.6268-0.394-0.5612.4075-2.28525.5110.1618-0.15220.6104-0.20020.0174-0.2632-0.78-0.3763-0.18860.4180.1311-0.02240.2603-0.02370.29065.692427.7702217.8464
621.6515-0.6506-0.58811.2402-0.33010.73270.20380.13570.1393-0.26460.00980.0576-0.63620.0232-0.12050.32290.04490.00390.2860.04350.21179.240424.3128212.305
634.65380.67781.38591.89880.30580.64850.0164-0.2386-0.34310.12560.0725-0.1370.22820.5005-0.12550.176-0.0141-0.02380.43490.01450.243618.807910.3216228.5076
642.7651-0.2055-0.00571.9173-0.42852.1130.0064-0.116-0.2622-0.08210.00610.14690.2505-0.04490.0020.1993-0.0229-0.03220.24920.01590.27310.49568.5873221.0726
655.75181.96670.16484.116-1.18271.88630.01560.2908-0.4596-0.7749-0.02750.08310.19750.4075-0.03920.39140.17360.02110.3680.01290.179616.73659.2113204.9255
660.4659-0.80140.00522.9124-1.68641.8577-0.02580.86850.9429-0.10030.0339-0.0373-0.95120.55730.03480.8033-0.14820.0930.85570.22540.522323.233131.8282202.5706
672.2481-0.29980.18151.9964-0.27622.69560.18170.5257-0.1254-0.26120.024-0.20230.34391.1846-0.1150.35890.18890.03070.6848-0.03140.245424.080812.7015205.9671
681.2176-0.8829-0.26061.20290.1790.30770.0042-0.0101-0.03050.082-0.0038-0.4754-0.04550.2309-0.19550.06660.76-0.02760.9838-0.18040.595728.83629.104206.1355
690.9165-0.0936-0.36141.2702-0.04151.29090.36350.7949-0.04630.0203-0.3147-0.21280.27420.5935-0.18280.23890.22530.01940.5656-0.02980.181216.651715.3288201.4014
702.79781.0626-3.09530.7526-1.72274.30410.25660.7423-0.277-0.3745-0.0070.28120.1421-0.6723-0.16940.23060.1301-0.05990.4562-0.08060.25940.749316.5218209.0868
711.0735-0.14490.30231.0336-0.42950.36760.21590.1092-0.0153-0.0319-0.20380.0818-0.03680.1243-0.08620.17220.1545-0.01120.3819-0.00550.20355.25115.947214.6403
723.3605-2.01120.27333.12171.77482.15420.29150.16320.237-0.3112-0.0902-0.69380.03160.5478-0.19730.44620.28370.04021.1031-0.04330.461326.27919.4353192.2797
732.7002-0.6525-0.46771.0681-0.0563.0080.18950.60760.62230.1658-0.1521-0.3162-0.8610.8601-0.21040.4441-0.0680.09060.56280.07450.30518.054625.2925204.85
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 66 )
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 87 )
5X-RAY DIFFRACTION5chain 'A' and (resid 88 through 117 )
6X-RAY DIFFRACTION6chain 'A' and (resid 118 through 127 )
7X-RAY DIFFRACTION7chain 'A' and (resid 128 through 150 )
8X-RAY DIFFRACTION8chain 'A' and (resid 151 through 159 )
9X-RAY DIFFRACTION9chain 'A' and (resid 160 through 190 )
10X-RAY DIFFRACTION10chain 'B' and (resid 15 through 65 )
11X-RAY DIFFRACTION11chain 'B' and (resid 66 through 78 )
12X-RAY DIFFRACTION12chain 'B' and (resid 79 through 117 )
13X-RAY DIFFRACTION13chain 'B' and (resid 118 through 127 )
14X-RAY DIFFRACTION14chain 'B' and (resid 128 through 150 )
15X-RAY DIFFRACTION15chain 'B' and (resid 151 through 168 )
16X-RAY DIFFRACTION16chain 'B' and (resid 169 through 190 )
17X-RAY DIFFRACTION17chain 'C' and (resid 15 through 62 )
18X-RAY DIFFRACTION18chain 'C' and (resid 63 through 72 )
19X-RAY DIFFRACTION19chain 'C' and (resid 73 through 117 )
20X-RAY DIFFRACTION20chain 'C' and (resid 118 through 150 )
21X-RAY DIFFRACTION21chain 'C' and (resid 151 through 190 )
22X-RAY DIFFRACTION22chain 'D' and (resid 15 through 26 )
23X-RAY DIFFRACTION23chain 'D' and (resid 27 through 36 )
24X-RAY DIFFRACTION24chain 'D' and (resid 37 through 52 )
25X-RAY DIFFRACTION25chain 'D' and (resid 53 through 62 )
26X-RAY DIFFRACTION26chain 'D' and (resid 63 through 72 )
27X-RAY DIFFRACTION27chain 'D' and (resid 73 through 98 )
28X-RAY DIFFRACTION28chain 'D' and (resid 99 through 117 )
29X-RAY DIFFRACTION29chain 'D' and (resid 118 through 127 )
30X-RAY DIFFRACTION30chain 'D' and (resid 128 through 150 )
31X-RAY DIFFRACTION31chain 'D' and (resid 151 through 168 )
32X-RAY DIFFRACTION32chain 'D' and (resid 169 through 190 )
33X-RAY DIFFRACTION33chain 'E' and (resid 15 through 62 )
34X-RAY DIFFRACTION34chain 'E' and (resid 63 through 72 )
35X-RAY DIFFRACTION35chain 'E' and (resid 73 through 117 )
36X-RAY DIFFRACTION36chain 'E' and (resid 118 through 127 )
37X-RAY DIFFRACTION37chain 'E' and (resid 128 through 150 )
38X-RAY DIFFRACTION38chain 'E' and (resid 151 through 168 )
39X-RAY DIFFRACTION39chain 'E' and (resid 169 through 190 )
40X-RAY DIFFRACTION40chain 'F' and (resid 15 through 62 )
41X-RAY DIFFRACTION41chain 'F' and (resid 63 through 117 )
42X-RAY DIFFRACTION42chain 'F' and (resid 118 through 150 )
43X-RAY DIFFRACTION43chain 'F' and (resid 151 through 190 )
44X-RAY DIFFRACTION44chain 'G' and (resid 15 through 61 )
45X-RAY DIFFRACTION45chain 'G' and (resid 62 through 71 )
46X-RAY DIFFRACTION46chain 'G' and (resid 72 through 117 )
47X-RAY DIFFRACTION47chain 'G' and (resid 118 through 190 )
48X-RAY DIFFRACTION48chain 'H' and (resid 15 through 26 )
49X-RAY DIFFRACTION49chain 'H' and (resid 27 through 36 )
50X-RAY DIFFRACTION50chain 'H' and (resid 37 through 52 )
51X-RAY DIFFRACTION51chain 'H' and (resid 53 through 62 )
52X-RAY DIFFRACTION52chain 'H' and (resid 63 through 78 )
53X-RAY DIFFRACTION53chain 'H' and (resid 79 through 117 )
54X-RAY DIFFRACTION54chain 'H' and (resid 118 through 127 )
55X-RAY DIFFRACTION55chain 'H' and (resid 128 through 150 )
56X-RAY DIFFRACTION56chain 'H' and (resid 151 through 168 )
57X-RAY DIFFRACTION57chain 'H' and (resid 169 through 190 )
58X-RAY DIFFRACTION58chain 'I' and (resid 15 through 62 )
59X-RAY DIFFRACTION59chain 'I' and (resid 63 through 72 )
60X-RAY DIFFRACTION60chain 'I' and (resid 73 through 117 )
61X-RAY DIFFRACTION61chain 'I' and (resid 118 through 127 )
62X-RAY DIFFRACTION62chain 'I' and (resid 128 through 150 )
63X-RAY DIFFRACTION63chain 'I' and (resid 151 through 168 )
64X-RAY DIFFRACTION64chain 'I' and (resid 169 through 190 )
65X-RAY DIFFRACTION65chain 'J' and (resid 15 through 26 )
66X-RAY DIFFRACTION66chain 'J' and (resid 27 through 48 )
67X-RAY DIFFRACTION67chain 'J' and (resid 49 through 66 )
68X-RAY DIFFRACTION68chain 'J' and (resid 67 through 77 )
69X-RAY DIFFRACTION69chain 'J' and (resid 78 through 117 )
70X-RAY DIFFRACTION70chain 'J' and (resid 118 through 127 )
71X-RAY DIFFRACTION71chain 'J' and (resid 128 through 150 )
72X-RAY DIFFRACTION72chain 'J' and (resid 151 through 159 )
73X-RAY DIFFRACTION73chain 'J' and (resid 160 through 190 )

+
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

+
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