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- PDB-4e2f: Crystal Structure of E. coli Aspartate Transcarbamoylase K164E/E2... -

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基本情報

登録情報
データベース: PDB / ID: 4e2f
タイトルCrystal Structure of E. coli Aspartate Transcarbamoylase K164E/E239K Mutant in an intermediate state
要素
  • Aspartate carbamoyltransferase catalytic chain
  • Aspartate carbamoyltransferase regulatory chain
キーワードTRANSFERASE/PROTEIN BINDING / transferase / cooperativity / allosteric transition / intermediate / TRANSFERASE-PROTEIN BINDING complex
機能・相同性
機能・相同性情報


aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding ...aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / identical protein binding / cytoplasm / cytosol
類似検索 - 分子機能
Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate/ornithine carbamoyltransferase ...Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate/ornithine carbamoyltransferase / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / SH3 type barrels. / Roll / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Aspartate carbamoyltransferase catalytic subunit / Aspartate carbamoyltransferase regulatory chain
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
手法X線回折 / 分子置換 / 解像度: 2.8 Å
データ登録者Guo, W. / Kantrowitz, E.R.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2012
タイトル: Trapping and structure determination of an intermediate in the allosteric transition of aspartate transcarbamoylase.
著者: Guo, W. / West, J.M. / Dutton, A.S. / Tsuruta, H. / Kantrowitz, E.R.
履歴
登録2012年3月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02012年5月2日Provider: repository / タイプ: Initial release
改定 1.12012年5月16日Group: Database references
改定 1.22012年5月30日Group: Database references
改定 1.32024年2月28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 / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ncs_dom_lim.selection_details / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
I: Aspartate carbamoyltransferase catalytic chain
K: Aspartate carbamoyltransferase catalytic chain
G: Aspartate carbamoyltransferase catalytic chain
C: Aspartate carbamoyltransferase catalytic chain
A: Aspartate carbamoyltransferase catalytic chain
D: Aspartate carbamoyltransferase regulatory chain
B: Aspartate carbamoyltransferase regulatory chain
E: Aspartate carbamoyltransferase catalytic chain
J: Aspartate carbamoyltransferase regulatory chain
L: Aspartate carbamoyltransferase regulatory chain
H: Aspartate carbamoyltransferase regulatory chain
F: Aspartate carbamoyltransferase regulatory chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)309,27718
ポリマ－308,88412
非ポリマー3926
水9,116506
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)124.086, 144.814, 203.359
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詳細
11A
21E
31I
41K
51G
61C
12D
22B
32J
42L
52H
62F

NCSドメイン領域:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEUchain A and (resseq 1:310 )AE1 - 3101 - 310
21ALAALALEULEUchain E and (resseq 1:310 )EH1 - 3101 - 310
31ALAALALEULEUchain I and (resseq 1:310 )IA1 - 3101 - 310
41ALAALALEULEUchain K and (resseq 1:310 )KB1 - 3101 - 310
51ALAALALEULEUchain G and (resseq 1:310 )GC1 - 3101 - 310
61ALAALALEULEUchain C and (resseq 1:310 )CD1 - 3101 - 310
12LYSLYSASNASNchain D and (resseq 13:153 )DF13 - 15313 - 153
22LYSLYSASNASNchain B and (resseq 13:153 )BG13 - 15313 - 153
32LYSLYSASNASNchain J and (resseq 13:153 )JI13 - 15313 - 153
42LYSLYSASNASNchain L and (resseq 13:153 )LJ13 - 15313 - 153
52LYSLYSASNASNchain H and (resseq 13:153 )HK13 - 15313 - 153
62LYSLYSASNASNchain F and (resseq 13:153 )FL13 - 15313 - 153

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
Aspartate carbamoyltransferase catalytic chain / Aspartate transcarbamylase / ATCase


分子量: 34337.105 Da / 分子数: 6 / 変異: K164E, E239K / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 株: K12 / 遺伝子: b4245, JW4204, pyrB / プラスミド: pEK695 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): EK1104 / 参照: UniProt: P0A786, aspartate carbamoyltransferase
#2: タンパク質
Aspartate carbamoyltransferase regulatory chain


分子量: 17143.625 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 株: K12 / 遺伝子: b4244, JW4203, pyrI / プラスミド: pEK695 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): EK1104 / 参照: UniProt: P0A7F3
#3: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Zn
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 506 / 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: 2.96 Å3/Da / 溶媒含有率: 58.41 %
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: 8.75
詳細: 16% (w/v) PEG 4000, 0.04 M Na2MoO4, 0.04 M N-cyclohexyl-3-aminopropanesulfonic acid, 30 mM Tris-acetate, pH 8.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: 回転陽極 / タイプ: RIGAKU MICROMAX-007 HF / 波長: 1.5418 Å
検出器タイプ: RIGAKU RAXIS IV++ / 検出器: IMAGE PLATE / 日付: 2008年6月19日 / 詳細: Rigaku Osmic VariMax
放射モノクロメーター: Rigaku Osmic VariMax / 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: 1.5418 Å / 相対比: 1
反射解像度: 2.8→29.89 Å / Num. all: 90709 / Num. obs: 83815 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 3.33 % / Biso Wilson estimate: 84.25 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 8.7
反射 シェル解像度: 2.8→2.9 Å / 冗長度: 3.35 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.2 / Num. unique all: 8981 / % possible all: 92.4

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解析

ソフトウェア
名称バージョン分類
CrystalClearデータ収集
MOLREP位相決定
PHENIX(phenix.refine: 1.7.2_869)精密化
d*TREKデータ削減
d*TREKデータスケーリング
精密化構造決定の手法: 分子置換 / 解像度: 2.8→29.888 Å / SU ML: 0.99 / σ(F): 1.34 / 位相誤差: 31.11 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2742 4207 5.02 %5% random
Rwork0.214 ---
obs0.2171 83783 92.4 %-
all-83904 --
溶媒の処理減衰半径: 1.11 Å / VDWプローブ半径: 1.3 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 50.111 Å2 / ksol: 0.275 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1-0.7772 Å20 Å2-0 Å2
2--2.9976 Å20 Å2
3----3.7748 Å2
精密化ステップサイクル: LAST / 解像度: 2.8→29.888 Å
タンパク質核酸リガンド溶媒全体
原子数21252 0 6 506 21764
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01421630
X-RAY DIFFRACTIONf_angle_d1.51129334
X-RAY DIFFRACTIONf_dihedral_angle_d18.1028040
X-RAY DIFFRACTIONf_chiral_restr0.0983414
X-RAY DIFFRACTIONf_plane_restr0.0063822
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A2415X-RAY DIFFRACTIONPOSITIONAL0.097
12E2415X-RAY DIFFRACTIONPOSITIONAL0.097
13I2415X-RAY DIFFRACTIONPOSITIONAL0.989
14K2415X-RAY DIFFRACTIONPOSITIONAL0.962
15G2415X-RAY DIFFRACTIONPOSITIONAL1.059
16C2415X-RAY DIFFRACTIONPOSITIONAL0.941
21D1105X-RAY DIFFRACTIONPOSITIONAL0.084
22B1105X-RAY DIFFRACTIONPOSITIONAL0.084
23J1105X-RAY DIFFRACTIONPOSITIONAL0.115
24L1105X-RAY DIFFRACTIONPOSITIONAL0.109
25H1105X-RAY DIFFRACTIONPOSITIONAL0.097
26F1105X-RAY DIFFRACTIONPOSITIONAL0.1
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.8-2.83180.44341480.38152499264789
2.8318-2.86510.42111240.36532646277093
2.8651-2.90.38761510.3272620277192
2.9-2.93670.40391340.30642655278993
2.9367-2.97530.34721450.30892613275892
2.9753-3.0160.39621310.29572654278593
3.016-3.05910.38441510.2922603275493
3.0591-3.10470.36361400.28422635277593
3.1047-3.15310.3891410.29222641278293
3.1531-3.20480.3371330.28642629276292
3.2048-3.260.36831420.26632628277093
3.26-3.31920.35421320.25852628276092
3.3192-3.38290.30571300.25682615274592
3.3829-3.45190.37571150.26342630274590
3.4519-3.52680.32951520.26092573272591
3.5268-3.60870.36581240.25272570269490
3.6087-3.69880.27381250.24942558268389
3.6988-3.79860.29711280.24982586271490
3.7986-3.91020.31761480.22932525267389
3.9102-4.03610.29411430.23232546268989
4.0361-4.180.30121280.21242502263088
4.18-4.34690.23131140.19132525263987
4.3469-4.5440.24451500.17092555270589
4.544-4.78270.21491300.14872627275791
4.7827-5.0810.24351500.1532759290996
5.081-5.47110.19511590.16412848300799
5.4711-6.01760.27411530.19432880303399
6.0176-6.87910.24861570.19662925308299
6.8791-8.63220.24931580.171529443102100
8.6322-29.8880.18451710.18472957212896
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)
10.7087-0.3803-0.19431.1975-0.69691.05660.1505-0.1491-0.0296-0.0253-0.16870.0550.12030.089600.2051-0.0285-0.03730.3659-0.02040.2425-30.4729-33.25727.0266
20.38890.0302-0.10390.6822-0.28711.20840.1121-0.21270.1749-0.1264-0.02710.1463-0.18480.176-00.22240.01310.00890.2955-0.00960.3124-32.0004-21.458516.269
31.6047-0.3815-0.22940.88-0.88421.6177-0.0331-0.43830.2378-0.0813-0.00080.1545-0.0275-1.0168-0.00060.3380.023-0.00020.8526-0.17630.4515-38.8252-19.905345.4521
40.1089-0.09720.53460.4804-0.64512.11750.8702-0.22050.4287-0.4896-0.40340.22640.13080.38750.1030.58570.13680.01120.7379-0.17520.808-26.7899-5.354546.4404
50.7244-0.38280.82750.362-0.48771.0495-0.0521-0.3392-0.0332-0.01210.1984-0.0973-0.01680.18650.00020.2849-0.0080.08390.53560.02470.3879-25.8709-27.323641.7225
61.48720.95040.42820.7213-0.21281.26990.02860.0354-0.0153-0.3177-0.04710.2011-0.22960.151-00.7731-0.0922-0.04230.40140.03410.3976-25.02433.94824.2784
70.56111.3024-0.64823.8534-0.83920.6890.8873-0.3121-0.9260.8437-0.4005-1.89930.20730.38740.43340.77870.0099-0.2640.37090.2050.5433-26.810616.964417.5353
81.62331.05310.03461.31770.00910.9514-0.25460.1982-0.0554-0.530.23750.2453-0.155-0.0207-0.010.6861-0.0996-0.07220.36920.03460.3355-28.288623.5042-3.8103
90.7774-0.44910.59810.2881-0.10770.338-0.09351.385-1.0775-1.07490.18760.015-0.09870.3877-0.00071.2711-0.119-0.01890.9737-0.34650.8698-18.632815.3406-17.8376
101.51720.33330.40530.0886-0.17170.754-0.1116-0.10280.0153-0.53730.20090.0148-0.33790.59510.00710.6469-0.16750.03710.33140.04170.4116-15.560829.1648-3.8171
111.09460.19150.12090.62010.23032.3271-0.215-0.4651-0.1928-0.177-0.0503-0.0437-0.2150.1519-00.7005-0.0574-0.0110.53410.06450.4731.462132.983518.6135
120.2971-0.16350.40190.0991-0.20550.3814-0.3019-0.6102-0.821-0.45540.50120.2993-0.3406-0.2620.13140.7195-0.12480.06380.4903-0.0180.9026-9.342316.963410.3557
130.2518-0.15350.42070.4665-0.7751.3902-0.09130.0439-0.0614-0.3817-0.1945-0.2899-0.03010.4503-0.00110.56160.02330.09240.56230.08590.59959.371521.970419.8477
140.7788-0.0084-0.17850.21360.00580.09040.0323-0.2571-0.17620.0237-0.5841-0.64250.4350.5807-01.00580.09520.04141.01440.25570.990415.953413.243435.2407
15-0.0254-0.1607-0.1840.30330.63210.9305-0.1311-0.4268-0.043-0.08420.4011-0.17830.1274-0.451700.7007-0.07110.0330.6990.05060.61173.277227.994730.8473
161.80950.04340.14440.7632-0.16580.1655-0.0371-0.22760.40170.4299-0.0365-0.0129-0.19350.067300.6970.0104-0.03330.4897-0.01480.4961-24.374733.861734.3775
170.2353-0.15550.15930.2066-0.18610.18290.07770.8033-0.3439-1.53840.13890.87650.7396-0.18680.05160.93030.0295-0.10660.52-0.15690.8139-12.460616.613329.049
181.55270.33520.95050.7583-0.08240.3590.0376-0.9113-0.11040.4206-0.01450.05940.0599-0.20820.05950.70510.00910.04530.66350.08690.4515-32.062922.6842.6474
191.10.7664-0.0860.472-0.01660.1427-0.0299-0.0356-0.2840.30690.16020.32370.7741-0.83470.00040.7396-0.22660.04760.97070.11160.9344-49.029615.030734.384
201.4067-1.0119-0.46840.8157-0.08110.791-0.04390.07860.2123-0.03640.21150.1198-0.3483-0.3551-00.74830.0391-0.04390.5940.06230.3886-36.256429.67129.9921
210.8114-0.1729-0.94471.6210.18081.350.0094-0.0091-0.09630.1534-0.05060.02410.09990.05060.00010.17170.001-0.01870.2874-0.0440.2264-0.2755-34.076626.3524
220.28810.2704-0.44231.2692-0.13390.5433-0.47350.27950.555-0.43070.41560.2917-0.3049-0.44890.03550.39910.1137-0.17340.37580.02230.7025-13.6298-16.876128.1279
231.4085-0.0861-0.54060.43850.20750.3381-0.0657-0.18620.205-0.04310.0747-0.0636-0.05940.155200.24010.0015-0.02440.3212-0.07430.265612.0431-22.739927.8037
240.3692-0.3074-0.40111.2988-0.49440.86930.3577-0.55590.67540.5105-0.36181.3729-0.20680.37330.01680.3243-0.1624-0.06390.6545-0.17510.717414.0841-8.693816.3547
251.3038-0.7253-0.81890.2760.06891.45880.0629-0.01710.1427-0.2614-0.03750.0050.05480.32530.00920.1951-0.0459-0.0820.2068-0.06620.284212.0554-26.257314.0068
261.3666-0.6112-0.08090.35730.06010.01080.5430.2697-0.30380.0409-0.4491-0.0955-0.89231.35960.01251.078-0.32330.00360.73350.16180.56180.60629.595879.792
270.1968-0.28160.14030.38-0.10690.25520.21460.3469-0.24120.07290.04370.1848-0.64210.411700.801-0.08260.00220.6076-0.00040.4161-3.72424.503767.8513
280.0838-0.22880.09230.704-0.15130.174-0.1549-0.0587-0.0031-0.0803-0.1843-0.1239-0.27070.5151-0.22260.85870.0947-0.0283-0.3671.3022-1.4445-4.1198-1.950376.7032
290.0002-0.0128-0.00140.0024-0.00840.0105-0.56370.1773-0.75640.32030.2354-0.2776-0.6290.374100.73150.002-0.00880.35420.03060.5697-12.4564-2.354379.9009
301.67221.0188-1.30931.2194-1.21051.34350.0254-0.93720.8414-0.2681-0.3905-0.9185-1.1540.6518-0.03511.4391-0.1027-0.07730.56410.00050.5704-0.458911.427674.5418
310.22510.1193-0.26170.23610.16590.77710.62260.02030.49830.4361-0.07790.4793-1.0941-0.16820.08061.10330.02670.05310.4790.00660.4987-10.6812.498573.1122
321.21010.55940.13811.1779-0.00691.0333-0.5639-0.22860.23520.67110.41770.54240.23221.3807-0.30831.02020.3850.14190.8053-0.05520.333-12.420612.897166.2052
330.02220.0282-0.08550.1869-0.15820.22210.0725-0.0113-0.08910.0475-0.28090.2595-0.55570.2044-00.79550.01960.01710.57540.05050.513-20.367713.046554.0402
340.44660.1254-0.53410.0352-0.16570.60310.2431.2403-0.2523-0.11040.11090.6346-0.7338-0.30910.05050.68290.04780.07430.4202-0.140.435-22.01334.458557.3235
350.8252-0.742-0.79650.57460.63661.1160.0152-0.18020.00340.4159-0.1406-0.0184-0.360.3477-00.4559-0.0742-0.11470.5590.08790.37415.2255-6.789170.8299
36-0.0457-0.26620.0970.70470.09350.96040.0285-0.1242-0.04780.0036-0.0584-0.0505-0.2093-0.0445-00.3419-0.05020.00780.5354-0.03020.42218.6441-13.32454.4627
370.85870.7863-0.09061.2208-0.4170.95760.0712-0.0033-0.0434-0.1371-0.1078-0.16660.070.014-00.23190.0026-0.01390.25830.02860.3494-15.9159-34.40550.5003
380.68810.1976-0.03680.0521-0.06560.11940.051-0.60820.30560.4661-0.25690.493-0.83820.0461-0.4120.6286-0.1363-0.12150.1541-0.17730.3347-7.2508-17.271810.9323
391.9342-0.0410.87740.2061-0.14830.25-0.17780.14740.1781-0.07250.0638-0.0901-0.1656-0.004100.2488-0.03230.00310.33550.03530.2767-20.3769-23.1567-11.145
400.88110.0681-0.14020.01140.09580.1995-0.15871.00970.73270.48050.0571-0.3757-1.2228-0.64580.10120.83670.0773-0.05840.4740.20910.6846-30.9175-8.709-7.5557
410.91860.0236-0.45280.75160.480.8572-0.1511-0.393-0.03290.07970.20070.151-0.1471-0.75290.01610.1004-0.033-0.00710.03060.01320.2649-32.4911-26.1679-4.3041
420.1548-0.00510.05930.9561-1.07851.17270.0040.0337-0.0573-0.14120.1099-0.0161-0.1934-0.09980.00010.36840.0167-0.04730.28380.06480.3562-72.0721-5.68398.8981
431.8013-0.26530.83570.27670.57180.5262-0.225-0.25490.522-0.15250.27750.0042-0.29980.09620.00040.5644-0.0011-0.02480.5348-0.04060.5164-59.4879-13.114819.2868
441.50020.7047-0.8670.8002-0.52850.6173-0.1113-0.02570.29450.19270.22660.1354-0.00040.088600.5550.0566-0.09990.30080.04670.3888-70.81967.13341.8036
450.54040.7744-0.03110.702-0.06440.9343-0.0711-0.20170.08540.03970.14760.0287-0.11030.0709-0.00030.6248-0.0238-0.14510.3575-0.00390.4034-55.003914.5936-2.3909
461.2663-0.62510.06841.50360.680.4824-0.11790.64320.6598-1.1415-0.3546-0.34980.2917-0.2339-1.01811.0369-0.1020.34580.8219-0.02710.88329.670310.5263-26.8502
470.29460.1492-0.04680.62450.68170.8333-0.0996-0.08250.4728-0.1756-0.0003-0.46580.13690.0895-00.5087-0.05690.2150.59750.0320.749123.56023.1728-17.6836
480.1742-0.1256-0.0080.33980.58181.50490.47140.74520.3707-0.13670.1051-0.9114-1.30431.14490.06150.6256-0.20240.18790.7272-0.00520.971629.80196.637-19.3902
490.43430.0565-0.30730.0933-0.13530.23450.7322-0.66660.9965-0.13070.1987-0.2976-0.46010.32460.01510.8951-0.31270.28410.8245-0.22241.041628.595413.3183-13.0774
500.2953-0.16770.22390.42130.26210.5715-0.34950.40160.1605-0.30730.5175-0.1267-0.4701-0.1851-0.06070.9783-0.39020.25550.7601-0.09371.104623.243613.3961-8.3731
510.13610.1687-0.22110.1857-0.32860.3964-0.44610.5203-0.05440.02420.10310.2282-0.14950.377400.7816-0.08310.07540.7026-0.05250.954416.052213.23464.2931
520.0578-0.03970.02070.0334-0.01480.031-0.7613-0.25131.054-0.1611-0.0069-0.6730.6258-0.4718-0.00081.4346-0.12520.26290.82070.11231.31720.28724.88194.2979
530.5611-0.1371-0.06930.33650.41590.37780.4039-0.35750.7329-0.162-0.2695-0.2366-0.21290.19670.00040.441-0.06410.12670.50720.12460.470620.9587-7.8976-23.1237
540.40160.31880.10060.20440.07390.17710.0430.3108-0.1235-0.89560.2673-0.4119-0.10010.41680.00030.615-0.05950.13760.47970.05720.525721.1336-5.6583-29.1135
550.42440.0943-0.42741.2528-0.3890.22310.08890.08090.0758-0.2669-0.1169-0.0777-0.37750.0123-0.08280.2397-0.0960.05260.46580.07120.390612.0837-15.0939-24.897
560.4961-0.0673-0.5770.04370.13440.61710.24880.22580.14780.0469-0.047-0.0111-0.0730.242800.3977-0.1074-0.02490.530.13490.6124-2.6663-13.1262-16.5157
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain I and (resseq 1:66)
2X-RAY DIFFRACTION2chain I and (resseq 67:134)
3X-RAY DIFFRACTION3chain I and (resseq 135:227)
4X-RAY DIFFRACTION4chain I and (resseq 228:253)
5X-RAY DIFFRACTION5chain I and (resseq 254:310)
6X-RAY DIFFRACTION6chain K and (resseq 1:66)
7X-RAY DIFFRACTION7chain K and (resseq 67:87)
8X-RAY DIFFRACTION8chain K and (resseq 88:195)
9X-RAY DIFFRACTION9chain K and (resseq 196:265)
10X-RAY DIFFRACTION10chain K and (resseq 266:310)
11X-RAY DIFFRACTION11chain G and (resseq 1:66)
12X-RAY DIFFRACTION12chain G and (resseq 67:87)
13X-RAY DIFFRACTION13chain G and (resseq 88:195)
14X-RAY DIFFRACTION14chain G and (resseq 196:265)
15X-RAY DIFFRACTION15chain G and (resseq 266:310)
16X-RAY DIFFRACTION16chain C and (resseq 1:66)
17X-RAY DIFFRACTION17chain C and (resseq 67:87)
18X-RAY DIFFRACTION18chain C and (resseq 88:212)
19X-RAY DIFFRACTION19chain C and (resseq 213:265)
20X-RAY DIFFRACTION20chain C and (resseq 266:310)
21X-RAY DIFFRACTION21chain A and (resseq 1:66)
22X-RAY DIFFRACTION22chain A and (resseq 67:87)
23X-RAY DIFFRACTION23chain A and (resseq 88:223)
24X-RAY DIFFRACTION24chain A and (resseq 224:242)
25X-RAY DIFFRACTION25chain A and (resseq 243:310)
26X-RAY DIFFRACTION26chain D and (resseq 10:19)
27X-RAY DIFFRACTION27chain D and (resseq 20:41)
28X-RAY DIFFRACTION28chain D and (resseq 42:50)
29X-RAY DIFFRACTION29chain D and (resseq 51:57)
30X-RAY DIFFRACTION30chain D and (resseq 58:67)
31X-RAY DIFFRACTION31chain D and (resseq 68:87)
32X-RAY DIFFRACTION32chain D and (resseq 88:114)
33X-RAY DIFFRACTION33chain D and (resseq 115:143)
34X-RAY DIFFRACTION34chain D and (resseq 144:153)
35X-RAY DIFFRACTION35chain B and (resseq 10:67)
36X-RAY DIFFRACTION36chain B and (resseq 68:153)
37X-RAY DIFFRACTION37chain E and (resseq 1:66)
38X-RAY DIFFRACTION38chain E and (resseq 67:87)
39X-RAY DIFFRACTION39chain E and (resseq 88:223)
40X-RAY DIFFRACTION40chain E and (resseq 224:242)
41X-RAY DIFFRACTION41chain E and (resseq 243:310)
42X-RAY DIFFRACTION42chain J and (resseq 10:67)
43X-RAY DIFFRACTION43chain J and (resseq 68:153)
44X-RAY DIFFRACTION44chain L and (resseq 10:67)
45X-RAY DIFFRACTION45chain L and (resseq 68:153)
46X-RAY DIFFRACTION46chain H and (resseq 10:19)
47X-RAY DIFFRACTION47chain H and (resseq 20:50)
48X-RAY DIFFRACTION48chain H and (resseq 51:67)
49X-RAY DIFFRACTION49chain H and (resseq 68:87)
50X-RAY DIFFRACTION50chain H and (resseq 88:114)
51X-RAY DIFFRACTION51chain H and (resseq 115:143)
52X-RAY DIFFRACTION52chain H and (resseq 144:153)
53X-RAY DIFFRACTION53chain F and (resseq 10:41)
54X-RAY DIFFRACTION54chain F and (resseq 42:67)
55X-RAY DIFFRACTION55chain F and (resseq 68:114)
56X-RAY DIFFRACTION56chain F and (resseq 115:153)

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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

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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://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

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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