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- PDB-7mtx: Crystal Structure of the Catalytic Domain of the Inosine Monophos... -

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基本情報

登録情報
データベース: PDB / ID: 7mtx
タイトルCrystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Bacillus anthracis in the complex with IMP and the inhibitor P176
要素Inosine-5'-monophosphate dehydrogenase
キーワードOXIDOREDUCTASE (酸化還元酵素) / IMPDH / TIM barrel (TIMバレル) / delta CBS / Structural Genomics (構造ゲノミクス) / Center for Structural Genomics of Infectious Diseases / CSGID / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
機能・相同性
機能・相同性情報


IMP dehydrogenase activity / IMPデヒドロゲナーゼ / GMP biosynthetic process / nucleotide binding / metal ion binding
類似検索 - 分子機能
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBSドメイン / CBSドメイン / CBS domain profile. / Aldolase-type TIM barrel
類似検索 - ドメイン・相同性
イノシン酸 / : / Chem-ZO4 / Inosine-5'-monophosphate dehydrogenase
類似検索 - 構成要素
生物種Bacillus anthracis (炭疽菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.44 Å
データ登録者Kim, Y. / Maltseva, N. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases / Center for Structural Genomics of Infectious Diseases (CSGID)
資金援助 米国, 1件
組織認可番号
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 米国
引用ジャーナル: To Be Published
タイトル: Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Bacillus anthracis in the complex with IMP and the inhibitor P176
著者: Kim, Y. / Maltseva, N. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
履歴
登録2021年5月13日登録サイト: RCSB / 処理サイト: RCSB
置き換え2021年6月9日ID: 5URR
改定 1.02021年6月9日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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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: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
E: Inosine-5'-monophosphate dehydrogenase
F: Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase
H: Inosine-5'-monophosphate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)332,58332
ポリマ-325,6778
非ポリマー6,90624
7,728429
1
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)166,29116
ポリマ-162,8384
非ポリマー3,45312
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area25080 Å2
ΔGint-120 kcal/mol
Surface area47840 Å2
手法PISA
2
E: Inosine-5'-monophosphate dehydrogenase
F: Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase
H: Inosine-5'-monophosphate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)166,29116
ポリマ-162,8384
非ポリマー3,45312
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area25110 Å2
ΔGint-114 kcal/mol
Surface area47850 Å2
手法PISA
単位格子
Length a, b, c (Å)85.390, 89.921, 104.856
Angle α, β, γ (deg.)81.413, 90.030, 83.443
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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要素

#1: タンパク質
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / IMPD / IMPDH


分子量: 40709.574 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Bacillus anthracis (炭疽菌)
遺伝子: guaB, BA_0008, A9486_01210, ABW01_29210, BVG01_30935, COL95_27530
プラスミド: pMCSG7 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): Gold / 参照: UniProt: A0A6H3A7R4, IMPデヒドロゲナーゼ
#2: 化合物
ChemComp-IMP / INOSINIC ACID / IMP / イノシン酸


分子量: 348.206 Da / 分子数: 8 / 由来タイプ: 合成 / : C10H13N4O8P
#3: 化合物
ChemComp-ZO4 / N-{2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenyl}-beta-D-ribopyranosylamine


分子量: 475.965 Da / 分子数: 8 / 由来タイプ: 合成 / : C24H30ClN3O5 / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物
ChemComp-K / POTASSIUM ION / カリウムカチオン


分子量: 39.098 Da / 分子数: 8 / 由来タイプ: 合成 / : K
#5: 水 ChemComp-HOH / water /


分子量: 18.015 Da / 分子数: 429 / 由来タイプ: 天然 / : H2O
研究の焦点であるリガンドがあるかY

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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: 2.43 Å3/Da / 溶媒含有率: 49.34 %
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: 6.2
詳細: 10 % (W/V) PEG8000, 0.1 M SODIUM/POTASSIUM PHOSPHATE PH 6.2, 0.2 M SODIUM CHLORIDE

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
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: 0.97926 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2014年5月29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: 0.97926 Å / 相対比: 1
反射解像度: 2.44→50 Å / Num. obs: 111274 / % possible obs: 98.6 % / 冗長度: 2.6 % / Biso Wilson estimate: 35.43 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 8.9
反射 シェル解像度: 2.44→2.49 Å / 冗長度: 2.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5504 / % possible all: 97.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19_4092精密化
HKL-3000データ削減
HKL-3000データスケーリング
HKL-3000位相決定
MOLREP位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4MJM
解像度: 2.44→40.08 Å / SU ML: 0.2833 / 交差検証法: FREE R-VALUE / σ(F): 1.98 / 位相誤差: 24.0567
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2223 5152 4.93 %
Rwork0.1779 99338 -
obs0.1801 104490 91.24 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 42.21 Å2
精密化ステップサイクル: LAST / 解像度: 2.44→40.08 Å
タンパク質核酸リガンド溶媒全体
原子数20621 0 456 429 21506
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.001621431
X-RAY DIFFRACTIONf_angle_d0.540329026
X-RAY DIFFRACTIONf_chiral_restr0.04183387
X-RAY DIFFRACTIONf_plane_restr0.0033706
X-RAY DIFFRACTIONf_dihedral_angle_d12.80727850
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.460.3031660.20961214X-RAY DIFFRACTION33.94
2.46-2.490.25851120.22482636X-RAY DIFFRACTION71.62
2.49-2.520.30741430.23032639X-RAY DIFFRACTION73.44
2.52-2.550.28951420.22932797X-RAY DIFFRACTION76.26
2.55-2.590.29321460.22382868X-RAY DIFFRACTION78.57
2.59-2.620.27741350.23252906X-RAY DIFFRACTION80.43
2.62-2.660.33571790.23233008X-RAY DIFFRACTION82.76
2.66-2.70.28441640.22243109X-RAY DIFFRACTION86.29
2.7-2.740.32061810.22133257X-RAY DIFFRACTION90.09
2.74-2.790.23441620.21963377X-RAY DIFFRACTION92.86
2.79-2.840.30811900.21583520X-RAY DIFFRACTION95.84
2.84-2.890.27041580.20813496X-RAY DIFFRACTION97.16
2.89-2.940.27561860.19833584X-RAY DIFFRACTION98.2
2.94-30.26171800.21493573X-RAY DIFFRACTION98.19
3-3.070.24941880.21493575X-RAY DIFFRACTION98.4
3.07-3.140.26971920.21713565X-RAY DIFFRACTION98.53
3.14-3.220.2811820.20373568X-RAY DIFFRACTION98.43
3.22-3.310.23641770.20043601X-RAY DIFFRACTION98.69
3.31-3.40.2492000.19693555X-RAY DIFFRACTION98.66
3.4-3.510.22711790.18793601X-RAY DIFFRACTION98.8
3.51-3.640.20922030.18483586X-RAY DIFFRACTION98.93
3.64-3.780.23761890.17253560X-RAY DIFFRACTION98.87
3.78-3.960.20181810.16133599X-RAY DIFFRACTION98.88
3.96-4.160.19462060.1423561X-RAY DIFFRACTION99.05
4.16-4.420.16551810.14013609X-RAY DIFFRACTION98.98
4.42-4.770.17731930.13543621X-RAY DIFFRACTION99.06
4.77-5.240.16081860.13243587X-RAY DIFFRACTION99.26
5.24-60.18572100.16423570X-RAY DIFFRACTION99.37
6-7.550.18331830.15783624X-RAY DIFFRACTION99.37
7.55-40.080.1731580.15213572X-RAY DIFFRACTION97.59
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)
12.822010808472.560101994350.7649445801964.355891055261.341516577421.12245158493-0.206631714446-0.354566318215-0.0820621193523-0.1962595796520.03215600422650.0495971930147-0.114961421095-0.04165301124750.1744717767980.266243641980.07052410397840.01135768528540.3282165681060.0243064401270.266023590078-15.14210066734.337056649866.04000245979
21.6072302296-0.1017521457640.09654396659792.79981118294-0.5272198261812.5903301659-0.03591682768890.228578747220.18647188638-0.306778969978-0.02164105528390.347263661993-0.159620977591-0.2114113263760.03110416047530.2771673292660.0473749245113-0.1222609192450.303727346530.03862782657090.401379433225-31.570752395112.62911256-18.9875785949
31.477848650060.1519225235060.8682863863370.1267581918990.09627130543252.446310310810.01250493886010.1800344277520.1871819012820.03361568161770.1817618821150.445166256082-0.377138942607-0.0670625923809-0.1858916318610.448406952510.108157605974-0.07345424026530.3461323758340.0350481085440.56905320799-30.781485939524.7406631116-13.3665475074
41.051816761880.2363238015670.469138757430.844308236682-0.0349571514720.723034870635-0.0427435980305-0.10882342950.210762572747-0.00960034498506-0.02082696387080.309311465932-0.142299701053-0.1751222533560.06135143593520.2864843053110.07834368446960.01570903860920.2399410550860.008975309370470.312926067657-24.538991171815.0048061929-3.47511113324
53.958184118280.0114704348781-0.648582433691.938652245321.360308027331.28063417837-0.2108466763290.565842607053-0.429031682623-0.4759046162920.155387800269-0.226271506587-0.044766733320.3055246617590.03825600142280.3980226468230.01164424900550.04055767272870.429165292772-0.01391153268080.303356753526-14.52066971936.93029095309-27.24799261
63.413352328081.114761745570.8716531978513.728962575722.375720432493.22615843394-0.2035581987270.4651989500070.561110807472-0.4512719564550.3037537493260.133031351382-0.6588481337250.194948606309-0.0637837738350.4095827213450.0321963435582-0.04404176099360.2648606567630.07133189432440.297948465039-11.416542431317.5191277903-21.3437428028
72.89389744962-0.330546915681-1.150479517892.54604297886-0.2230148373643.05367826432-0.2263929468080.481721545-0.443537199523-0.108364494325-0.2245595084190.2424260712590.0677971854253-0.3728471728350.3658567680280.271686939809-0.0147417567398-0.105802742310.253894253661-0.02629576968040.335211333495-26.1274957174-5.82428715535-13.3488992299
81.73468296282-0.3905239767010.5591224719972.384554485740.3258519318471.863446573830.002564692918610.03365538430220.0652618646696-0.08832309031530.06034396821030.09054070070440.0123488492812-0.0347739322881-0.04300125584320.250797097614-0.007727582819450.02188698939050.2351913114180.07501093935640.266099639595-16.4558910956-6.87451364624-5.92098296002
94.88150966316-2.390139752290.3929812065422.12373197966-0.2209344438851.304764874660.17251447084-0.130594371079-0.2866348754670.0222337337595-0.0831580941730.42183986997-0.157768790778-0.0719314495998-0.09943405776960.334148250733-0.002832343099920.01580692166990.218793375827-0.004238521082750.29314591756-7.80640805486-10.903858541310.3380380535
102.209043425410.05460922437631.057953559851.836073125350.2292175840292.903059725890.00255013464140.042989407215-0.137776495364-0.0860949424496-0.02056069054840.1666514356890.44268358012-0.1103782173780.01503773031950.3688612452030.000825155922613-0.003173075886830.2068959096140.01426994050760.317467623209-11.4894625565-36.4668631718-6.80300694939
110.7024702972660.06658006059090.03938939088771.708524492470.2346786190991.085994070380.0161180938585-0.109285995599-0.08369003929770.122533906849-0.004821086045070.3713204126680.0917551972534-0.250765895637-0.004500599587130.273680795983-0.009829446885270.02640593878010.2561398880260.03704135799770.340445019328-18.8282604592-25.25903065911.18609309863
122.03600110168-0.69513122104-0.06004068335542.291865732350.1925314150291.869639728270.08755563555080.383419691032-0.102078694095-0.614079694043-0.07351098347920.04665837637930.166311777614-0.0874055706121-0.008094631999820.330535704155-0.0300238622998-0.006001645357630.248820388856-0.01481398765590.250287592266-8.2450325106-22.4715924745-16.0845077965
130.98140844619-0.5676439614710.1359000833411.687824517580.6518397831791.199247227180.03419112753820.0480882852477-0.02166260771710.0392989253080.0157059361607-0.07785705938840.5196117341050.0557637385728-0.03184104510340.304796374112-0.001665557099010.01083895114480.2103236131680.01391462618790.2825218661233.48142614129-27.5717739186-5.80346228535
142.677232334940.937302759334-0.6191666078041.94438605204-0.4513811909491.98412357827-0.0598584712599-0.0898049841635-0.092148348876-0.00963340003064-0.0167583156201-0.03206340475260.1974795005620.2451408875160.07197881070570.282027475840.0627337130861-0.04363366936190.185969785513-0.0002089138737520.228864762695.95772034247-17.63927213284.03065249564
155.32001431921-0.4378265383931.724056237372.56977604003-0.8922728119074.7011170398-0.171254631122-0.286135880815-0.5961069324710.6839090571920.3851914445490.290751167805-0.205562045708-0.0487993088650.001558490346230.4537836804120.054783740020.01960849247330.223778189374-0.02925519310860.2223330062119.901002661223.8892389455422.0769842475
162.902720179451.29169472737-0.6670823144211.154622745130.01401085605261.385884416030.1985370505350.04849265239540.2672440282030.0432615704255-0.0728386684535-0.0307688427056-0.3599813673280.144063743613-0.1286999350450.3791796642610.000641250075021-0.0142599326270.207636327584-0.003017839365430.34559247966510.976156659933.5421730674-2.25838308023
170.7793525126440.369572616903-0.7707991087123.27442842368-1.269233708552.22500546987-0.0993412808829-0.1283619120380.2685999283270.1327359998720.00238791579108-0.579865740889-0.3068818759780.507047415890.06869181482280.438525837041-0.103793573856-0.09363182407270.420830033303-0.08607353143880.47654933427623.591346103633.43768975926.84192186238
181.063618315850.2638561798550.3042960619911.527111417830.2002179390610.885017973118-0.0417512424293-0.2129738892540.187837914760.282690906746-0.04921079673510.0165113620532-0.242567104130.0847620013520.08842031109210.35424960237-0.00978784072824-0.02345495640940.236947085206-0.02444070078710.2498672477412.077006674624.352643841110.2091832943
191.37235099897-0.748936985967-0.3502064875561.585497823750.06740592700383.618234992230.02836872882220.09862042121940.088813905041-0.128516907106-0.16131606212-0.226206999266-0.01051878790380.3035819962740.1247729647830.248530377532-0.03958262760180.008210915680030.1937603183710.009493189909280.20930097960617.380840940920.6918546636-10.5092709277
205.488149401130.631223998148-2.710028203020.903916033537-0.6333912089462.792480511530.297072258091-0.01596649298840.3572392734690.3727726063760.036811766706-0.0700967117664-0.582788792122-0.270267876346-0.3210001882050.3858830811380.0568965716255-0.03006159643330.190856246489-0.01875068317860.34604854978-3.3071068727928.8150120019-7.42767284986
211.83585989742-0.172339880431-0.2451944571751.493200368-0.1860038629422.570135222040.0046767246061-0.0325213905810.00629716597286-0.00419422599470.03801539365080.08297302061540.03039141235530.0237725885844-0.05835523799740.2670228143440.0353474518852-0.005788072866930.2080001882290.01038709844870.347037134448-6.0009619486217.4473523144-3.98335809995
221.943819205642.058005923570.6398175216553.410559145250.454005804710.820235793503-0.1865527415840.003242208463040.2094590902490.07175737813270.1017598805540.325388453567-0.151457199681-0.06679969818680.08055595231770.2992375733490.088545498641-0.01505961603380.243659322995-0.02927391101180.2140387321896.29676732603-3.033121977715.4794753612
231.55326774675-0.2018274733010.01382793088622.98180483328-0.2176530791751.98027163806-0.0559600119846-0.0966786316129-0.1723304653140.115152887872-0.0209902075351-0.4967518375290.2870323852880.5384556074810.06685685638070.2896457284540.123330823531-0.05491329288140.473275969772-0.009742858905520.37513420412235.2350181317-15.380960376610.2212096844
243.7137239060.02701024097880.6871131461311.015644315530.4512919089231.001009915780.1051918470240.0298673428627-0.4099276677490.0615795306432-0.064243064528-0.02340244451790.4647637355420.368051883111-0.02920455806850.4412739353630.114902777053-0.09307948662810.3127390136980.05965152042640.3546427755925.1616072854-24.614263920918.9312591882
250.976417454485-0.4350993937960.1437247191911.57121230925-0.2970038383151.32554856569-0.031882427983-0.0170736883542-0.112109360390.122425139754-0.039942570902-0.1303730383660.06204955419020.1605922377280.07003032118260.3071166737610.035630135135-0.04061566737790.2939630224810.01652758241550.24228667283518.0194617512-12.052575914415.5228871331
261.579539662241.20126774422-0.2969417164422.345645918510.07370386613992.77535628595-0.1607394553650.502946843688-0.17832188675-0.3483277830390.265317748777-0.291606775391-0.01512281375750.162557475971-0.1647920904760.2796605374030.00181921067252-0.04759790900690.4415215373480.004103593603360.34505260303227.6375642508-9.55291010767-4.11282917176
271.40503099970.228994033278-0.6281718743530.561262000271-0.03751227893011.7726671885-0.1874063234580.0589263573937-0.13284550992-0.02930962519690.10615695233-0.1430038943290.1239428779410.2491277937310.02265084676130.2703827832670.036095704109-0.05514554583070.3181653514550.03136953396160.25655715255124.7372778728-9.167848875080.163764283069
282.13829915533-0.134709808897-0.2917912904271.84416731918-0.964878231531.989258479710.04908027242060.00240454582313-0.1763088856680.0219281021208-0.0674851914788-0.0514461767925-0.1818915410370.03665742503060.03618985033190.276415060148-0.0041521452017-0.04849769904180.126838815009-0.01332191635930.22255890345216.36422583056.910936874145.71288906243
290.9175392952180.2809292268580.01839859920141.24872230998-0.01556507641350.4344019457310.0694304893627-0.0773148100420.003074360557590.223255263605-0.01064664453170.1207103617630.00335193491123-0.016882493749-0.07400237355730.321883376302-0.0344851289810.05000828292950.398057819592-0.04435947493040.21253806108820.495106345117.813033244363.9249317459
302.29853060639-0.376498814240.2024276100373.6037555913-0.2308493798122.84955423456-0.09715891209140.05871119621680.313106308069-0.258518884227-0.1004275369920.512918008891-0.284008418726-0.6479583826750.1721753752350.285772501320.0876058784935-0.0246474582930.460517105152-0.09075496425590.3717548134381.8715433437331.005343253554.2444356426
313.896025117880.183230023962-0.9466107303630.308691669229-0.4237057610530.9080240989750.0757885385347-0.2076964292420.290333361793-0.0818130495693-0.2136198250530.0996169782065-0.368692223824-0.1905576141790.1196361793560.3542060566750.02709723092190.03206378394620.362594765989-0.1230917330380.39406392796313.476205379238.096571532262.3872479967
326.04778203141-2.85865188727-1.353984491992.608882890450.3045931539142.345434085280.2122184313170.07664520843480.1610216838630.311151511224-0.2093524099610.215297320268-0.220411839325-0.3536522866960.01719519074890.342659543646-0.01513365525960.06648087136630.387522003936-0.146923370420.33975591620316.803630453833.629646267567.0815410832
330.467843125956-0.280050927125-0.5864765262610.5523804549230.1795593248851.27731429995-0.0217582230893-0.1370078093280.05717165377640.0650108552336-0.1185008398080.282996679267-0.00739275438834-0.17398279550.126328591510.301435337813-0.02319152709190.02592176565810.376563084863-0.06935242453120.28711632509520.978048534621.351323563460.5881675493
341.137512215781.16534123579-0.4219378400841.935441988481.230835477464.27263232891-0.311328230350.926790661704-0.138956648748-0.9617007142810.2508899948610.1805572263890.498118595855-0.4456470528870.06967539074170.534223032237-0.0680269316872-0.05789901382420.601356968952-0.1083514841640.317087143899.769731037216.400757021838.1316305141
354.479593306132.47449084189-0.7775539365393.61032981505-0.1373618155691.95845132859-0.2450462907230.344465882870.589022101903-0.3097891064240.08801618621620.69146462538-0.229631267568-0.2046100746890.1103157194320.2739294383670.00579281713346-0.04136592469290.3242578703780.003416358041840.23288217724317.255500677826.894037639440.9306906265
361.80553859604-1.031930269631.167277948332.25356663978-1.814531036953.87219513460.0219319887684-0.201125510875-0.008434859195560.105799104733-0.06401288394650.2886073932260.226930013181-0.5215435772780.02128808948690.243423757168-0.08480071178180.03082728963460.391238212806-0.03813953928660.3192318967810.81094049655.9530232169959.9485797211
373.255717184530.3561506399740.3183915370131.907510293330.415373631732.003690213290.145098302962-0.08777269894350.1977860674680.000445783833582-0.0463730542362-0.003160339982690.08381753671170.0391852166029-0.06555155398450.280090769143-0.04662599511930.04667084037510.2923855662260.03524790716150.25117272542522.82280954094.2168995793459.0819050491
382.56040038125-0.5347505195471.631999971517.226334315382.447346608733.27360477456-0.234699763587-0.3393017092370.4356078456671.184164067230.0285190263655-0.2398010876140.18929220998-0.245468755250.2347743928150.392645462941-0.0383877102019-0.04525444823450.3826746996820.007694611492060.23075418094729.324941496712.034621092274.0998227915
392.771572744190.848897174958-0.1296099291231.549844919930.007662972348561.448454297940.0311463729356-0.277525980567-0.4614933430310.11546864105-0.06983214303180.1775417826950.301383138976-0.1281585858420.040513887880.347497426854-0.0118141170027-0.004902126562920.3129353077450.05100074459370.35031707156426.7968177686-23.772232420560.4238568473
400.7239397025071.085488477960.2034228938295.13290814124-0.3465993279680.322384403830.232902772944-0.353217422224-0.320302149010.557643412048-0.446760725710.2555485134250.308142770693-0.2343057578710.2455736687880.387865869281-0.05383620975960.07728558746930.4741066879210.09017125563860.38973512208317.3746757102-16.791694427672.5726106619
411.3366355143-0.114205258766-0.7530058180070.926387785674-0.8463014475211.12230577501-0.0763010811197-0.274975241444-0.1242775158550.208660381151-0.0405531766826-0.08596126723610.137856878528-0.02090523342990.09638384771420.359773986211-0.0547105717554-0.01218595877660.3575209738170.031600777460.25770395995729.7755695646-10.901026553665.9311222019
424.00906954838-1.40633221073-1.518013773720.6512896403610.7002829569026.75351207609-0.1129344378490.72906956208-0.26857687385-0.14952889799-0.07041536664820.340298215449-0.13996835996-0.4241136814880.1515789647330.334829739205-0.0283034604175-0.05588673076770.378379025606-0.05418784517920.32847569685723.1543434034-16.75315162740.4595367313
432.46210411947-1.6826062559-1.591025088515.058058242461.840811411183.36492878385-0.0188263521964-0.159318160062-0.3038163509480.164982281712-0.250862636010.649793169591-0.0156118203673-0.5545919835070.2922122970790.222454039429-0.0440724056313-0.01767949158630.374418731327-0.04228600818740.29981312945115.643593823-9.7840252652150.001672905
444.921846432061.591767095352.962039668321.509763142711.186802880282.548789458290.264752254276-0.0333809946892-0.467925340440.001310325745060.0242936381147-0.08762199034770.4600674129380.158787276065-0.2934377989470.373752181955-0.00399924077038-0.01821513280830.2913232114870.04774052816130.30946028718342.881794727-20.257956373353.0382280286
452.29805487257-0.0393056214018-0.6423579947662.056064428490.7195967261472.33749487243-0.0345049107431-0.02193353554510.009066058923770.02834134462680.05745248388530.05091173518610.05807743779450.161597607348-0.0429278752690.1792133971830.0143254673786-0.01390375163130.3131016946020.03306253320940.30716289155345.3179793792-8.349563574652.883331366
464.64060745283-3.67488240733-0.00813484042283.824542729810.7084640462340.8348596921290.02030791323590.2410823991720.0219102437970.311849317891-0.166959099242-0.069012014529-0.04093974582480.1003662759270.1623208188070.275140025381-0.0752521024320.04495535817460.2879968138940.008383800492560.24679017762546.626526259323.113026310458.1105723034
472.872042462380.33422525753-0.6053946431291.213687373760.2421895822111.943593715880.01758720769980.2250373601670.272235730551-0.272977327347-0.0348313086619-0.324874345031-0.3571598985620.323583977997-0.004837453738940.466776481741-0.09446107545190.07656563455390.3811737264440.07213591263810.42307691146551.704843234542.804391762233.8001211977
480.0415057502809-0.2405449911280.1741540317215.38359226296-1.763539001761.320246966970.114647805320.07470297340760.364154343190.227438675989-0.130806810365-0.206970921195-0.39269254550.521575977182-0.01989104153250.402603248752-0.1609341735480.09860349567370.5236869787280.03339451476160.57070430516465.168709335137.946731953641.3229591332
491.123787351160.0621699763783-0.06001937662041.74173482753-0.1733451532450.9368780451830.06473713999810.07158036799310.2421895091350.0496520553183-0.0287233815368-0.213821332452-0.2232380695530.264558101096-0.0300973062360.268199338503-0.1116946861620.03010881627990.341201564001-0.01063009361280.30102267851951.767346808532.11398855145.741984676
503.74846042356-1.307272514371.431727516653.34547518865-1.248104698091.542727832270.1271450001590.2425255822080.0669767696269-0.443588883599-0.0550113476159-0.199315253390.1152683141020.460837669783-0.085251072160.346887833195-0.02682112298060.02561878214410.429549330122-0.04496182850710.20585713821446.199610600223.41096977526.4183849976
511.540465425430.00802502189427-0.4919640563221.06237763771-0.423220070541.36337743931-0.0625004256811-0.08737381725230.0399722067813-0.08999387614470.000840045519070.0651626413109-0.0910821150792-0.1258219342050.04765976489540.293885761757-0.04115232902480.03713080609290.265274954441-0.02874933850620.24781212883133.072002897130.195592486448.4459802535
521.39981047691.21688790528-1.058645499042.82606528078-1.530710919051.6580607473-0.0564448496486-0.2115881986520.1832995868760.0613389028703-0.0834387327238-0.236744605313-0.02958839719520.1364132224280.1174545249990.218728814448-0.0024566756291-0.04478360133940.507397078927-0.0928011655770.33221585959854.26601623877.3351616372758.5554370052
531.01487904025-0.5045302633480.6778881794212.75370187964-0.1501104851031.26818264450.04834463136430.112929039409-0.155247828215-0.194807042169-0.0305749180778-0.3601207755840.1385110658430.390688202419-0.03299586111220.3146682656150.05376033983730.1105385664990.549428919565-0.05505568580460.45779808067470.8396923684-7.7363011920537.1297007018
542.62461018825-0.143305517978-2.109633359390.9992091779870.09578644889213.283092737550.118341067375-0.49187748051-0.773189266271-0.247530318797-0.157045263589-0.01076593105220.2810931730180.539687988840.01122715384350.3762272886040.13957615138-0.03350862125570.5813318739480.05831764097790.50964253327370.2572686232-17.628492551146.0584221499
550.268957506423-0.0336002135325-0.2264807481021.23469574836-0.01289272674120.8300654276160.00520115415328-0.208291522909-0.01512207611060.124756131778-0.0172090184531-0.2923386419340.1197764248740.2869929302710.01461794564140.2666939950330.0285750706483-0.03550944708240.4715085385390.009431751897360.31630255928163.7884012759-5.4786317882152.6621682687
563.028597900670.9060100070330.04337898941272.63180149321-1.009906051572.97683082733-0.181809565920.652943508915-0.255042737691-0.778966272850.251737342432-0.1682447090190.5866542488180.232098447206-0.05401987523560.471964036973-0.01113094283270.00616675284940.434387764777-0.02587095783340.30552246763153.3045602327-7.9450350500530.0164501201
571.843834926810.51089995141-0.5998365887751.40654576445-0.07574146828281.23155207319-0.03632918337670.215242095443-0.195472264878-0.2820867781340.059377682298-0.3657243335230.09902125032680.212630518438-0.0195407378580.3163004506750.04467756639150.01189653489620.4526311263310.02116209252890.27119754529358.20061890920.90674319455636.0704224833
581.67204079669-0.2795189205910.1329808950072.26132908408-0.2619923999452.625982924620.013796665937-0.0825662039511-0.12441086431-0.06414070345960.00999995278487-0.101943647973-0.1243096096510.147122058829-0.0470336168670.260610443058-0.05852425566970.05308240485070.31674504803-0.05839620679250.32150521500855.450002769414.591662998943.7244412361
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 26 )AA-1 - 261 - 28
22chain 'A' and (resid 27 through 232 )AA27 - 23229 - 107
33chain 'A' and (resid 233 through 257 )AA233 - 257108 - 132
44chain 'A' and (resid 258 through 363 )AA258 - 363133 - 238
55chain 'A' and (resid 364 through 389 )AA364 - 389239 - 264
66chain 'A' and (resid 390 through 427 )AA390 - 427265 - 291
77chain 'A' and (resid 428 through 446 )AA428 - 446292 - 310
88chain 'A' and (resid 447 through 486 )AA447 - 486311 - 350
99chain 'B' and (resid -1 through 26 )BE-1 - 261 - 28
1010chain 'B' and (resid 27 through 232 )BE27 - 23229 - 107
1111chain 'B' and (resid 233 through 355 )BE233 - 355108 - 230
1212chain 'B' and (resid 356 through 418 )BE356 - 418231 - 282
1313chain 'B' and (resid 419 through 445 )BE419 - 445283 - 309
1414chain 'B' and (resid 446 through 486 )BE446 - 486310 - 350
1515chain 'C' and (resid -4 through 12 )CI-4 - 121 - 17
1616chain 'C' and (resid 13 through 232 )CI13 - 23218 - 110
1717chain 'C' and (resid 233 through 257 )CI233 - 257111 - 135
1818chain 'C' and (resid 258 through 355 )CI258 - 355136 - 233
1919chain 'C' and (resid 356 through 427 )CI356 - 427234 - 295
2020chain 'C' and (resid 428 through 446 )CI428 - 446296 - 314
2121chain 'C' and (resid 447 through 486 )CI447 - 486315 - 354
2222chain 'D' and (resid -2 through 26 )DM-2 - 261 - 29
2323chain 'D' and (resid 27 through 242 )DM27 - 24230 - 118
2424chain 'D' and (resid 243 through 270 )DM243 - 270119 - 146
2525chain 'D' and (resid 271 through 355 )DM271 - 355147 - 231
2626chain 'D' and (resid 356 through 389 )DM356 - 389232 - 265
2727chain 'D' and (resid 390 through 446 )DM390 - 446266 - 311
2828chain 'D' and (resid 447 through 486 )DM447 - 486312 - 351
2929chain 'E' and (resid -3 through 56 )EQ-3 - 561 - 60
3030chain 'E' and (resid 57 through 242 )EQ57 - 24261 - 119
3131chain 'E' and (resid 243 through 270 )EQ243 - 270120 - 147
3232chain 'E' and (resid 271 through 293 )EQ271 - 293148 - 170
3333chain 'E' and (resid 294 through 368 )EQ294 - 368171 - 245
3434chain 'E' and (resid 369 through 389 )EQ369 - 389246 - 266
3535chain 'E' and (resid 390 through 427 )EQ390 - 427267 - 293
3636chain 'E' and (resid 428 through 446 )EQ428 - 446294 - 312
3737chain 'E' and (resid 447 through 486 )EQ447 - 486313 - 352
3838chain 'F' and (resid -4 through 12 )FU-4 - 121 - 17
3939chain 'F' and (resid 13 through 242 )FU13 - 24218 - 120
4040chain 'F' and (resid 243 through 270 )FU243 - 270121 - 148
4141chain 'F' and (resid 271 through 368 )FU271 - 368149 - 246
4242chain 'F' and (resid 369 through 389 )FU369 - 389247 - 267
4343chain 'F' and (resid 390 through 427 )FU390 - 427268 - 296
4444chain 'F' and (resid 428 through 446 )FU428 - 446297 - 315
4545chain 'F' and (resid 447 through 486 )FU447 - 486316 - 355
4646chain 'G' and (resid -1 through 26 )GY-1 - 261 - 28
4747chain 'G' and (resid 27 through 242 )GY27 - 24229 - 117
4848chain 'G' and (resid 243 through 270 )GY243 - 270118 - 145
4949chain 'G' and (resid 271 through 376 )GY271 - 376146 - 251
5050chain 'G' and (resid 377 through 427 )GY377 - 427252 - 290
5151chain 'G' and (resid 428 through 486 )GY428 - 486291 - 349
5252chain 'H' and (resid -1 through 26 )HH-1 - 261 - 28
5353chain 'H' and (resid 27 through 232 )HH27 - 23229 - 107
5454chain 'H' and (resid 233 through 257 )HH233 - 257108 - 132
5555chain 'H' and (resid 258 through 363 )HH258 - 363133 - 238
5656chain 'H' and (resid 364 through 398 )HH364 - 398239 - 273
5757chain 'H' and (resid 399 through 446 )HH399 - 446274 - 309
5858chain 'H' and (resid 447 through 486 )HH447 - 486310 - 349

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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

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