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- PDB-7ta1: Human Ornithine Aminotransferase (hOAT) soaked with gamma-Aminobu... -

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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: 7ta1
タイトルHuman Ornithine Aminotransferase (hOAT) soaked with gamma-Aminobutyric acid
要素Ornithine aminotransferase, mitochondrial
キーワードTRANSFERASE / Human Ornithine Aminotransferase / hOAT / OAT / PLP / GABA / gamma-aminobutyric acid / soaking
機能・相同性
機能・相同性情報


arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding / cytoplasm
類似検索 - 分子機能
Ornithine aminotransferase / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
類似検索 - ドメイン・相同性
PYRIDOXAL-5'-PHOSPHATE / Chem-PLZ / Ornithine aminotransferase, mitochondrial
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.2 Å
データ登録者Butrin, A. / Wawrzak, Z. / Liu, D.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Cancer Institute (NIH/NCI)1R01CA260250-01 米国
引用ジャーナル: J.Biol.Chem. / 年: 2022
タイトル: Determination of the pH dependence, substrate specificity, and turnovers of alternative substrates for human ornithine aminotransferase.
著者: Butrin, A. / Butrin, A. / Wawrzak, Z. / Moran, G.R. / Liu, D.
履歴
登録2021年12月20日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年5月4日Provider: repository / タイプ: Initial release
改定 1.12022年6月8日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
改定 1.22023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Ornithine aminotransferase, mitochondrial
B: Ornithine aminotransferase, mitochondrial
C: Ornithine aminotransferase, mitochondrial
D: Ornithine aminotransferase, mitochondrial
E: Ornithine aminotransferase, mitochondrial
F: Ornithine aminotransferase, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)293,39312
ポリマ－291,5626
非ポリマー1,8316
水16,141896
1
A: Ornithine aminotransferase, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,9282
ポリマ－48,5941
非ポリマー3341
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Ornithine aminotransferase, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,9282
ポリマ－48,5941
非ポリマー3341
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Ornithine aminotransferase, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,9282
ポリマ－48,5941
非ポリマー3341
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Ornithine aminotransferase, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,9282
ポリマ－48,5941
非ポリマー3341
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: Ornithine aminotransferase, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,8412
ポリマ－48,5941
非ポリマー2471
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: Ornithine aminotransferase, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,8412
ポリマ－48,5941
非ポリマー2471
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)114.607, 114.607, 349.326
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDモデル要素
11B-689-

HOH

21C-672-

HOH

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 38 through 63 or resid 65...
d_2ens_1(chain "B" and (resid 38 through 63 or resid 65...
d_3ens_1(chain "C" and (resid 38 through 63 or resid 65...
d_4ens_1(chain "D" and (resid 38 through 63 or resid 65...
d_5ens_1(chain "E" and (resid 38 through 63 or resid 65...
d_6ens_1(chain "F" and (resid 38 through 63 or resid 65...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROGLUA3 - 28
d_12ens_1GLYGLYA30 - 40
d_13ens_1LYSASPA42 - 71
d_14ens_1LEUTHRA73 - 93
d_15ens_1LEUTYRA95 - 131
d_16ens_1ALAGLYA133 - 144
d_17ens_1THRLEUA146 - 211
d_18ens_1GLYARGA213 - 215
d_19ens_1LEUTHRA217 - 219
d_110ens_1HISHISA221
d_111ens_1VALARGA223 - 239
d_112ens_1LEUGLUA241 - 306
d_113ens_1GLUALAA308 - 311
d_114ens_1ASNMETA313 - 326
d_115ens_1LEUGLYA328 - 338
d_116ens_1GLYILEA340 - 347
d_117ens_1GLUTHRA349 - 350
d_118ens_1ASPILEA352 - 385
d_119ens_1GLUILEA387 - 394
d_120ens_1ILEASNA396 - 398
d_121ens_1THRPHEA400 - 404
d_21ens_1PROGLUC3 - 28
d_22ens_1GLYGLYC30 - 40
d_23ens_1LYSASPC42 - 71
d_24ens_1LEUTHRC73 - 93
d_25ens_1LEUTYRC95 - 131
d_26ens_1ALAGLYC133 - 144
d_27ens_1THRLEUC146 - 211
d_28ens_1GLYARGC213 - 215
d_29ens_1LEUTHRC217 - 219
d_210ens_1HISHISC221
d_211ens_1VALARGC223 - 239
d_212ens_1LEUGLUC241 - 306
d_213ens_1GLUALAC308 - 311
d_214ens_1ASNMETC313 - 326
d_215ens_1LEUGLYC328 - 338
d_216ens_1GLYILEC340 - 347
d_217ens_1GLUTHRC349 - 350
d_218ens_1ASPILEC352 - 385
d_219ens_1GLUILEC387 - 394
d_220ens_1ILEASNC396 - 398
d_221ens_1THRPHEC400 - 404
d_31ens_1PROGLUE3 - 28
d_32ens_1GLYGLYE30 - 40
d_33ens_1LYSASPE42 - 71
d_34ens_1LEUTHRE73 - 93
d_35ens_1LEUTYRE95 - 131
d_36ens_1ALAGLYE133 - 144
d_37ens_1THRLEUE146 - 211
d_38ens_1GLYARGE213 - 215
d_39ens_1LEUTHRE217 - 219
d_310ens_1HISHISE221
d_311ens_1VALARGE223 - 239
d_312ens_1LEUGLUE241 - 306
d_313ens_1GLUALAE308 - 311
d_314ens_1ASNMETE313 - 326
d_315ens_1LEUGLYE328 - 338
d_316ens_1GLYILEE340 - 347
d_317ens_1GLUTHRE349 - 350
d_318ens_1ASPILEE352 - 385
d_319ens_1GLUILEE387 - 394
d_320ens_1ILEASNE396 - 398
d_321ens_1THRPHEE400 - 404
d_41ens_1PROGLUG1 - 26
d_42ens_1GLYGLYG28 - 38
d_43ens_1LYSASPG40 - 69
d_44ens_1LEUTHRG71 - 91
d_45ens_1LEUTYRG93 - 129
d_46ens_1ALAGLYG131 - 142
d_47ens_1THRLEUG144 - 209
d_48ens_1GLYARGG211 - 213
d_49ens_1LEUTHRG215 - 217
d_410ens_1HISHISG219
d_411ens_1VALARGG221 - 237
d_412ens_1LEUGLUG239 - 304
d_413ens_1GLUALAG306 - 309
d_414ens_1ASNMETG311 - 324
d_415ens_1LEUGLYG326 - 336
d_416ens_1GLYILEG338 - 345
d_417ens_1GLUTHRG347 - 348
d_418ens_1ASPILEG350 - 383
d_419ens_1GLUILEG385 - 392
d_420ens_1ILEASNG394 - 396
d_421ens_1THRPHEG398 - 402
d_51ens_1PROGLUI3 - 28
d_52ens_1GLYGLYI30 - 40
d_53ens_1LYSASPI42 - 71
d_54ens_1LEUTHRI73 - 93
d_55ens_1LEUTYRI95 - 131
d_56ens_1ALAGLYI133 - 144
d_57ens_1THRLEUI146 - 211
d_58ens_1GLYARGI213 - 215
d_59ens_1LEUTHRI217 - 219
d_510ens_1HISHISI221
d_511ens_1VALARGI223 - 239
d_512ens_1LEUGLUI241 - 306
d_513ens_1GLUALAI308 - 311
d_514ens_1ASNMETI313 - 326
d_515ens_1LEUGLYI328 - 338
d_516ens_1GLYILEI340 - 347
d_517ens_1GLUTHRI349 - 350
d_518ens_1ASPILEI352 - 385
d_519ens_1GLUILEI387 - 394
d_520ens_1ILEASNI396 - 398
d_521ens_1THRPHEI400 - 404
d_61ens_1PROGLUK2 - 27
d_62ens_1GLYGLYK29 - 39
d_63ens_1LYSASPK41 - 70
d_64ens_1LEUTHRK72 - 92
d_65ens_1LEUTYRK94 - 130
d_66ens_1ALAGLYK132 - 143
d_67ens_1THRLEUK145 - 210
d_68ens_1GLYARGK212 - 214
d_69ens_1LEUTHRK216 - 218
d_610ens_1HISHISK220
d_611ens_1VALARGK222 - 238
d_612ens_1LEUGLUK240 - 305
d_613ens_1GLUALAK307 - 310
d_614ens_1ASNMETK312 - 325
d_615ens_1LEUGLYK327 - 337
d_616ens_1GLYILEK339 - 346
d_617ens_1GLUTHRK348 - 349
d_618ens_1ASPILEK351 - 384
d_619ens_1GLUILEK386 - 393
d_620ens_1ILEASNK395 - 397
d_621ens_1THRPHEK399 - 403

NCS oper:
IDCodeMatrixベクター
1given(-0.467111201002, -0.86554962012, -0.180640474444), (0.7886411671, -0.500221443021, 0.357524289381), (-0.399815251652, 0.024543085609, 0.916267101611)62.0881625356, 88.2607778301, 15.6957044773
2given(-0.447359540495, 0.866945335598, -0.21971624112), (0.807846995215, 0.497112640438, 0.31664215613), (0.383735161081, -0.035844215721, -0.92274726678)-115.746952175, -6.12128101681, 277.693043676
3given(-0.385922664649, 0.819440132151, -0.423770653457), (-0.902284707203, -0.430982308461, -0.0116857580469), (-0.192213433603, 0.377851981092, 0.905694140606)-37.4412900711, 98.517879104, -14.9529946766
4given(-0.526845016615, -0.84962875396, 0.0237762257953), (-0.849631073021, 0.527213967803, 0.0131328561152), (-0.0236932105181, -0.0132820404367, -0.999631041523)99.8727207084, -5.62781884659, 293.416262951
5given(0.980567259532, -0.0273632681091, 0.194265542731), (0.10001853423, 0.921597938816, -0.375038040712), (-0.168772457305, 0.387180178636, 0.906425599223)-14.2713158005, 19.8479443579, -73.2608450312

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要素

#1: タンパク質
Ornithine aminotransferase, mitochondrial / Ornithine delta-aminotransferase / Ornithine--oxo-acid aminotransferase


分子量: 48593.668 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: OAT / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P04181, ornithine aminotransferase
#2: 化合物
ChemComp-PLZ / 4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]BUTANOIC ACID / 4-[[(2-メチル-5-[(ホスホノオキシ)メチル]-3-ヒドロキシピリジン-4-イル)メチル]アミノ]酪酸


分子量: 334.262 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C12H19N2O7P / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物 ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / ピリドキサ-ル5′-りん酸


分子量: 247.142 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C8H10NO6P / タイプ: SUBJECT OF INVESTIGATION
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 896 / 由来タイプ: 天然 / 式: 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: 2.27 Å3/Da / 溶媒含有率: 45.85 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.8
詳細: Once hOAT was purified, it was transferred to a 10 kDa centrifugal filter tube and concentrated to ~6 mg/mL. The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. ...詳細: Once hOAT was purified, it was transferred to a 10 kDa centrifugal filter tube and concentrated to ~6 mg/mL. The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition contained 8% PEG 6000, 100 mM NaCl, 5% glycerol, and 50 mM Tricine pH 7.8. Once holoenzyme crystals reached their maximum size within seven days, 1 uL of 10 mM GABA was added to the drop with crystals. The crystals were soaked for different time periods from 50 minutes to 2.5 hours. After soaking, crystals were transferred into a cryoprotective solution (well solution supplemented with 30% glycerol), and then flash-frozen in liquid nitrogen.

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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: 21-ID-D / 波長: 1.1271 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2021年7月3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: 1.1271 Å / 相対比: 1
反射解像度: 2.01→99.25 Å / Num. obs: 177531 / % possible obs: 99.8 % / 冗長度: 6.1 % / CC1/2: 0.993 / Net I/σ(I): 6.7
反射 シェル解像度: 2.01→2.12 Å / Num. unique obs: 25577 / CC1/2: 0.417 / % possible all: 99.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
autoPROCデータ削減
Aimless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: 1OAT

1oat


解像度: 2.2→99.25 Å / 交差検証法: FREE R-VALUE / σ(F): 23.78 / 位相誤差: 38.5163
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2681 6888 5.08 %
Rwork0.2508 128647 -
obs0.2552 135535 99.79 %
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: 39.81 Å2
精密化ステップサイクル: LAST / 解像度: 2.2→99.25 Å
タンパク質核酸リガンド溶媒全体
原子数18951 0 118 896 19965
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.004519512
X-RAY DIFFRACTIONf_angle_d0.818226510
X-RAY DIFFRACTIONf_chiral_restr0.05212927
X-RAY DIFFRACTIONf_plane_restr0.00533416
X-RAY DIFFRACTIONf_dihedral_angle_d13.6667188
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.576883510836
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.538152694275
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.590135556529
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.551605232119
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.585264487432
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.3373310.31596307X-RAY DIFFRACTION94.86
2.24-2.280.33933160.30736392X-RAY DIFFRACTION95.13
2.28-2.320.32993850.29776320X-RAY DIFFRACTION94.12
2.32-2.370.32373410.28856376X-RAY DIFFRACTION94.81
2.37-2.420.3323360.28276350X-RAY DIFFRACTION94.85
2.42-2.480.32793790.2826308X-RAY DIFFRACTION94.12
2.48-2.540.31143190.27946431X-RAY DIFFRACTION95.12
2.54-2.610.3153320.2726423X-RAY DIFFRACTION95.03
2.61-2.690.29753320.27096371X-RAY DIFFRACTION94.91
2.69-2.770.28813690.27436280X-RAY DIFFRACTION93.24
2.77-2.870.29573230.26876410X-RAY DIFFRACTION94.63
2.87-2.990.29613350.2656388X-RAY DIFFRACTION94.95
2.99-3.120.29593150.26296468X-RAY DIFFRACTION95.33
3.12-3.290.27023740.25396431X-RAY DIFFRACTION94.49
3.29-3.490.25783580.24596415X-RAY DIFFRACTION94.71
3.49-3.760.22453220.2316487X-RAY DIFFRACTION95.17
3.76-4.140.24293770.23226492X-RAY DIFFRACTION94.47
4.14-4.740.2373510.21716529X-RAY DIFFRACTION94.86
4.74-5.970.22533080.2336592X-RAY DIFFRACTION94.99
5.97-99.250.27923700.25696892X-RAY DIFFRACTION94.79
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)
10.00609282980754-0.0049057515232-0.004242791320770.0116944061374-0.005438810912480.0151856062020.0161407581873-0.0149535575626-0.000269268576343-0.0199279931712-0.005755469702710.001248433248730.05563602513280.02140160535250.007379695318510.2823118719070.1050824968650.002086788944620.1117072723970.04257961376660.731266455454-22.3670682695104.529391624175.909288671
20.032200902227-0.02812387708740.02408752539050.0104625867081-0.00475041535911-0.01556320751040.01015806680410.0487457718878-0.00486551180379-0.02248967933070.0185717359715-0.02212585284770.00795248056351-0.01385918987590.0821150676905-0.4063204543330.4436722667540.00964000099794-0.165631742168-0.04400396410351.01881535539-12.7425362513122.509825435152.778254665
30.00241654901593-0.000984340415169-0.0004911563760320.0043900533388-0.004268257185380.0281892362265-0.0154883395727-0.000870049834072-0.00704935231801-0.0255108935676-0.01613697554770.0006130941833290.04858551569110.006638926285820.002419874403230.2924215471550.0627236358301-0.04384071219780.217439487582-0.05272984589570.875367502519-15.2543028718102.440373208151.787750469
40.01935653896180.0478965409887-0.002147293914270.110415219784-0.0008948251764190.02399899762090.0495033853905-0.02845603630590.01443115339430.06666865649740.01216845071690.0657050638644-0.00393834806792-0.03939211766550.02367415813240.210768925246-0.03618246913970.002147614674180.1183899886260.02238944775150.934309088638-33.5118466742103.091034782160.306710209
50.00356871891860.000769892281528-0.004186700462120.000257055827377-0.0006456844249220.00448775771476-0.0213090722242-0.03303083979630.02774628233710.0171642469886-0.00482470413211-0.019752831793-0.01424214543660.00571424569497-0.01311216537780.1705766806750.084522402689-0.06608315259620.152777031954-0.04100267790370.573058932735-55.156106589378.9557724201194.020199681
60.006326816573210.003262295039420.00222647333440.00834573224605-0.00247491271034-0.002174578880130.01728749411010.007954941761360.0486421794796-0.005207772650290.0664903724015-0.0100097727145-0.004590740097050.01686291069850.1140966861810.0469082301101-0.1386957656560.01454978028550.004399379044910.007828090239910.943890128787-57.682381099686.4498285905169.133641531
70.0165712685131-0.0208021856952-0.004335326483710.0145959343419-0.00147460365972-0.006113307930070.004335794625330.00113089968170.02128295212590.000145249142793-0.04319975488730.01969901118740.01567494461510.00411913625529-0.0875181699929-0.2305006082450.2702006605730.0265767792472-0.04824313141020.02711958871860.872203759455-65.16502191764.3120581058164.127395431
80.07969076059510.0530237891371-0.02246458841510.0518133804128-0.0108318186280.0166925288083-0.024360492163-0.0251742359945-0.0394571984572-0.0354358630860.0229460095350.01338950120260.03183353581720.03589013828160.04507310263910.05464689043170.0601489465826-0.003676932401710.1088621194160.03982511722890.812136350366-52.763561276973.2530562224166.91897104
90.0138903060838-0.0149058431928-0.007159004135870.01212219077920.001294910729560.0119194782932-0.0106479506641-0.0337205872637-0.006403764855490.00397162315720.04245961886830.01888375728270.017641088366-0.0006239220450550.02439707943810.02280482606910.0883973774327-0.03734159301990.220367286981-0.00732599506970.807704655064-40.07497387171.1990417203179.084159301
100.00167422723625-0.000764816818188-0.001161370622360.00709138113483-0.000613910910442-0.0028276267051-0.001309584711460.0225551590372-0.0170011010719-0.02182166150050.01996290674610.009304568103550.00276073962213-0.02863226615290.01271280445480.165073166149-0.146504739697-0.02499951045760.1224269432060.0399702740560.726898659114-53.678721970483.5492291389103.00341217
110.0128777301665-0.0105388486746-0.008341438409310.01345500986680.01054553071320.004769132020470.01775869452750.005310708775840.01388827084680.01451291253280.01517201133090.03259732944320.000676591823484-0.03306158786710.02940892801870.1405786967830.05601328930580.01989368718730.0580309346170.01099888542620.777942718712-52.435304828898.6144896292126.854627847
120.00465208482634-0.0118358663127-0.008170612290380.0383703064560.00742531741445-0.000699350583552-0.02216391023990.0224141583235-0.06333736473810.0166806323913-0.01981012806920.0144035265840.0762542042309-0.0260863400505-0.01545157029930.1586046340370.05475793151110.0280448454818-0.3767810349140.0264137655511.10668188807-34.461764107591.0139039948127.720431392
130.008982238405270.01971721377370.006807508602330.03856049547180.009719191865210.006110961033290.01242073831480.0551343199278-0.0157456404142-0.06080838050440.0540970928864-0.002143351476640.0332205584376-0.00458798123130.07895235795170.188971990825-0.196739656051-0.07123193515480.0280248423630.05904959142161.03526105508-47.358695119768.9629195442115.864203162
140.00131924553681-0.00928360632637-0.001342435660970.01660194206540.007198706425890.00412328620026-0.00859781207161-0.003038905299720.05757217997630.03266454682670.0668038325480.007618545178050.0156016023930.008594166640320.02711931906890.1451581592710.09114583376810.02637366235610.1606832448780.05626951366550.826302155183-17.296230261771.5762785551187.880844349
150.0408738781419-0.0358920162806-0.001069806281150.0669315799645-0.00299157743080.00607892150680.02850501750110.03312726509060.034643894193-0.05015418161480.04952312270250.0521446285028-0.0243572932703-0.0191236309680.141450539303-0.3143745573320.183456469054-0.03064850607620.0919027376109-0.002378157720571.157017762783.0695442977655.4771580271172.186543913
160.0530955142077-0.0150284841625-0.01385448085840.007918567280080.000986694168971-4.7798121309E-50.01139597854810.003480671529390.04637575623070.01037369033970.0346203115496-0.013831311347-0.041731410599-0.02430859759990.09219951221130.04954452433420.0511290417814-0.01217309112820.2068550161350.06368047511670.973813165938-9.1610154687277.3887563763172.074654358
170.0560346769971-0.056808257436-0.008170853562850.06587851573260.002282317025380.007713691633690.01617017111750.03576814590170.02160363288990.00806464279832-0.0196188731871-0.005799665451370.001894336185990.0395451549055-0.000206564001040.0998208823658-0.05520185285120.01446162890150.07114748778330.01509026067490.86431445771720.875163961864.6973354728121.52244497
180.00388465646524-0.003972998195390.007871310398810.02099028545160.00626156404258-0.01000531610370.0170841187381-0.05795617131290.0108534299164-0.00331188770860.0269134941772-0.0461777736584-0.0428747012701-0.002046911816710.06833070039390.05569731381380.176153542657-0.0158877947342-0.2500571505570.06358445034390.9219865954744.1444256174177.750421292141.561370324
190.008058498721820.00759062295030.007054510791960.0758805827532-0.0003229660379360.004434491229270.0129554155342-0.0300191813549-0.01516623071180.03141913048550.01094602475380.02651235049320.01605494715220.05038656726280.06077399795310.0852064042910.1276615694010.0151722349691-0.09239807824230.02749238473390.89569398659517.828329750669.7674759148139.474940268
200.00218040248768-0.000531121272349-0.002519943097510.000156637388753-0.001954138043450.0157620346851-0.00539891666392-0.01658207073530.00381584434279-0.0243174332170.01063239328410.00413718362362-0.0302198762780.001464128128190.01400421387930.07579870489320.0504749525134-0.04077958457320.138608735864-0.0008999861515250.76389244201234.442320612476.0225042626130.821524762
210.00145523454383-0.000294869274283-0.0005189620240140.001729195630780.001538416599680.00437169874428-0.0204207073765-0.00644381098711-7.06240434271E-50.014977361261-0.0322445941857-0.01385875493370.001195870167620.00157712737399-0.01502625095820.137347582701-0.02026893247750.003439879061740.1383029105950.04934731786160.702811595805-5.6793190372451.6631742853137.711684355
220.0364077458046-0.034748239582-0.02114360250780.0405546684869-0.00774886520787-8.59904685907E-5-0.00825859471604-0.00397049019426-0.0019524467134-0.0004818936022920.0144686654619-0.0330574129623-0.003072821918310.06811105755930.003126187818110.1332461335820.115499687847-0.0532179850296-0.08336160665750.01889280407750.8695094165457.4933380378858.4605539366116.295248821
230.000815234219087-0.000756983317668-0.0005544996925060.050925358708-0.0154081966114-0.001854595958010.008477402281670.01877868314150.00775622499774-0.0218554483676-0.006628193730210.01085713794750.00809506039957-0.0135815244754-0.001618567058360.1159072512620.0125715611751-0.0324450612731-0.09025263734250.03742230756110.857491853589-7.5687461353681.990557295120.67736108
240.00179166575478-0.00117472881795-0.0009058972846270.0008740208618120.000685131683507-0.0005611430113380.0191728452380.03141431297760.0159260305636-0.00615888683262-0.01919707739070.00889776085403-0.00631288931719-0.007079164937520.01682522039940.1423497232840.0401211566481-0.0383200345070.07870123407090.00699775635370.662356330181-10.366462873578.5868268027109.543196187
250.0828147376227-0.01567769992010.01292635981080.01736427798350.001933297405720.008930566038060.02306556739040.0444455295093-0.00991065078977-0.04018200817330.01340169098890.01114178789830.034202511291-0.04294534356790.05121765231330.1284994016230.110735556612-0.0279180267865-0.0883228045026-0.02651233712850.954174429801-4.4390481144863.5501444343111.371754002
260.01439678344110.01344103369920.003515602074140.0205816312561-0.006397896465130.01264040001150.0131104150963-0.0102338369756-0.0152473312374-0.01628852426040.03837418468670.0503767650727-0.0125503980882-0.018766230480.03658705616980.248157086673-0.05478557257320.01047335375060.130082946155-0.06182415870750.923918175439-16.059930294448.9271941475117.890171074
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 36 through 82 )AA36 - 821 - 47
22chain 'A' and (resid 83 through 326 )AA83 - 32648 - 291
33chain 'A' and (resid 327 through 362 )AA327 - 362292 - 327
44chain 'A' and (resid 363 through 439 )AA363 - 439328 - 404
55chain 'B' and (resid 36 through 61 )BC36 - 611 - 26
66chain 'B' and (resid 62 through 141 )BC62 - 14127 - 106
77chain 'B' and (resid 142 through 301 )BC142 - 301107 - 266
88chain 'B' and (resid 302 through 389 )BC302 - 389267 - 354
99chain 'B' and (resid 390 through 439 )BC390 - 439355 - 404
1010chain 'C' and (resid 36 through 82 )CE36 - 821 - 47
1111chain 'C' and (resid 83 through 141 )CE83 - 14148 - 106
1212chain 'C' and (resid 142 through 344 )CE142 - 344107 - 309
1313chain 'C' and (resid 345 through 439 )CE345 - 439310 - 404
1414chain 'D' and (resid 38 through 82 )DG38 - 821 - 45
1515chain 'D' and (resid 83 through 326 )DG83 - 32646 - 289
1616chain 'D' and (resid 327 through 439 )DG327 - 439290 - 402
1717chain 'E' and (resid 36 through 117 )EI36 - 1171 - 82
1818chain 'E' and (resid 118 through 263 )EI118 - 26383 - 228
1919chain 'E' and (resid 264 through 389 )EI264 - 389229 - 354
2020chain 'E' and (resid 390 through 439 )EI390 - 439355 - 404
2121chain 'F' and (resid 37 through 61 )FK37 - 611 - 25
2222chain 'F' and (resid 62 through 141 )FK62 - 14126 - 105
2323chain 'F' and (resid 142 through 220 )FK142 - 220106 - 184
2424chain 'F' and (resid 221 through 263 )FK221 - 263185 - 227
2525chain 'F' and (resid 264 through 389 )FK264 - 389228 - 353
2626chain 'F' and (resid 390 through 439 )FK390 - 439354 - 403

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万見について

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お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る