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- PDB-6lpi: Crystal Structure of AHAS holo-enzyme -

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基本情報

登録情報
データベース: PDB / ID: 6lpi
タイトルCrystal Structure of AHAS holo-enzyme
要素(Acetolactate synthase isozyme 1 ...) x 2
キーワードRECOMBINATION / AHAS / allosteric regulation
機能・相同性
機能・相同性情報


acetolactate synthase regulator activity / acetolactate synthase complex / acetolactate synthase / branched-chain amino acid biosynthetic process / acetolactate synthase activity / valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / magnesium ion binding / cytosol
類似検索 - 分子機能
Acetolactate synthase, small subunit / AHAS, ACT domain / Acetolactate synthase, large subunit, biosynthetic / Acetolactate synthase large subunit, TPP binding domain / ACT domain / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / ACT domain profile. / ACT domain / Thiamine pyrophosphate enzyme, central domain ...Acetolactate synthase, small subunit / AHAS, ACT domain / Acetolactate synthase, large subunit, biosynthetic / Acetolactate synthase large subunit, TPP binding domain / ACT domain / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / ACT domain profile. / ACT domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / ACT-like domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily
類似検索 - ドメイン・相同性
FLAVIN-ADENINE DINUCLEOTIDE / THIAMINE DIPHOSPHATE / Acetolactate synthase isozyme 1 large subunit / Acetolactate synthase isozyme 1 small subunit
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.849 Å
データ登録者Zhang, Y. / Yang, X. / Xi, Z. / Shen, Y.
引用ジャーナル: Biochem.J. / 年: 2020
タイトル: Molecular architecture of the acetohydroxyacid synthase holoenzyme.
著者: Zhang, Y. / Li, Y. / Liu, X. / Sun, J. / Li, X. / Lin, J. / Yang, X. / Xi, Z. / Shen, Y.
履歴
登録2020年1月10日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02020年11月18日Provider: repository / タイプ: Initial release
改定 1.12023年11月29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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
E: Acetolactate synthase isozyme 1 small subunit
A: Acetolactate synthase isozyme 1 large subunit
F: Acetolactate synthase isozyme 1 small subunit
B: Acetolactate synthase isozyme 1 large subunit
G: Acetolactate synthase isozyme 1 small subunit
C: Acetolactate synthase isozyme 1 large subunit
H: Acetolactate synthase isozyme 1 small subunit
D: Acetolactate synthase isozyme 1 large subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)301,48720
ポリマ－296,5478
非ポリマー4,94112
水905
1
E: Acetolactate synthase isozyme 1 small subunit
A: Acetolactate synthase isozyme 1 large subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)75,3725
ポリマ－74,1372
非ポリマー1,2353
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
F: Acetolactate synthase isozyme 1 small subunit
B: Acetolactate synthase isozyme 1 large subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)75,3725
ポリマ－74,1372
非ポリマー1,2353
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
G: Acetolactate synthase isozyme 1 small subunit
C: Acetolactate synthase isozyme 1 large subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)75,3725
ポリマ－74,1372
非ポリマー1,2353
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
4
H: Acetolactate synthase isozyme 1 small subunit
D: Acetolactate synthase isozyme 1 large subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)75,3725
ポリマ－74,1372
非ポリマー1,2353
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)111.173, 104.577, 118.535
Angle α, β, γ (deg.)90.000, 105.680, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and ((resid 11 through 12 and (name N...
21(chain B and (resid 11 through 28 or resid 30...
31(chain C and (resid 11 through 28 or resid 30...
41(chain D and (resid 11 through 28 or resid 30...

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSARGARG(chain A and ((resid 11 through 12 and (name N...AB11 - 1211 - 12
12LYSLYSTPPTPP(chain A and ((resid 11 through 12 and (name N...AB - J11 - 60211
13LYSLYSTPPTPP(chain A and ((resid 11 through 12 and (name N...AB - J11 - 60211
14LYSLYSTPPTPP(chain A and ((resid 11 through 12 and (name N...AB - J11 - 60211
15LYSLYSTPPTPP(chain A and ((resid 11 through 12 and (name N...AB - J11 - 60211
21LYSLYSILEILE(chain B and (resid 11 through 28 or resid 30...BD11 - 2811 - 28
22ILEILESERSER(chain B and (resid 11 through 28 or resid 30...BD30 - 4730 - 47
23SERSERILEILE(chain B and (resid 11 through 28 or resid 30...BD49 - 5249 - 52
24SERSERTPPTPP(chain B and (resid 11 through 28 or resid 30...BD - M8 - 6028
25SERSERTPPTPP(chain B and (resid 11 through 28 or resid 30...BD - M8 - 6028
26SERSERTPPTPP(chain B and (resid 11 through 28 or resid 30...BD - M8 - 6028
27SERSERTPPTPP(chain B and (resid 11 through 28 or resid 30...BD - M8 - 6028
28SERSERTPPTPP(chain B and (resid 11 through 28 or resid 30...BD - M8 - 6028
29SERSERTPPTPP(chain B and (resid 11 through 28 or resid 30...BD - M8 - 6028
31LYSLYSILEILE(chain C and (resid 11 through 28 or resid 30...CF11 - 2811 - 28
32ILEILESERSER(chain C and (resid 11 through 28 or resid 30...CF30 - 4730 - 47
33SERSERILEILE(chain C and (resid 11 through 28 or resid 30...CF49 - 5249 - 52
34HISHISSERSER(chain C and (resid 11 through 28 or resid 30...CF54 - 11554 - 115
35GLUGLUGLUGLU(chain C and (resid 11 through 28 or resid 30...CF124124
36LYSLYSTPPTPP(chain C and (resid 11 through 28 or resid 30...CF - P11 - 60211
37LYSLYSTPPTPP(chain C and (resid 11 through 28 or resid 30...CF - P11 - 60211
38LYSLYSTPPTPP(chain C and (resid 11 through 28 or resid 30...CF - P11 - 60211
39LYSLYSTPPTPP(chain C and (resid 11 through 28 or resid 30...CF - P11 - 60211
41LYSLYSILEILE(chain D and (resid 11 through 28 or resid 30...DH11 - 2811 - 28
42ILEILESERSER(chain D and (resid 11 through 28 or resid 30...DH30 - 4730 - 47
43SERSERILEILE(chain D and (resid 11 through 28 or resid 30...DH49 - 5249 - 52
44HISHISSERSER(chain D and (resid 11 through 28 or resid 30...DH54 - 11554 - 115
45GLUGLUGLUGLU(chain D and (resid 11 through 28 or resid 30...DH124124
46LYSLYSTPPTPP(chain D and (resid 11 through 28 or resid 30...DH - S11 - 60211
47LYSLYSTPPTPP(chain D and (resid 11 through 28 or resid 30...DH - S11 - 60211
48LYSLYSTPPTPP(chain D and (resid 11 through 28 or resid 30...DH - S11 - 60211
49LYSLYSTPPTPP(chain D and (resid 11 through 28 or resid 30...DH - S11 - 60211

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要素

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Acetolactate synthase isozyme 1 ... , 2種, 8分子 EFGHABCD

#1: タンパク質
Acetolactate synthase isozyme 1 small subunit / Acetohydroxy-acid synthase I small subunit / ALS-I


分子量: 13640.341 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: ilvN, b3670, JW3645 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P0ADF8, acetolactate synthase
#2: タンパク質
Acetolactate synthase isozyme 1 large subunit / AHAS-I / Acetohydroxy-acid synthase I large subunit / ALS-I


分子量: 60496.316 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: ilvB, b3671, JW3646 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P08142, acetolactate synthase

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非ポリマー , 4種, 17分子

#3: 化合物
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / FAD


分子量: 785.550 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C27H33N9O15P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: FAD*YM
#4: 化合物
ChemComp-TPP / THIAMINE DIPHOSPHATE / 3-[(4-アミノ-2-メチル-5-ピリミジニル)メチル]-4-メチル-5-[2-(ホスホノオキシホスフィナトオキシ)(以下略)


分子量: 425.314 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C12H19N4O7P2S / タイプ: SUBJECT OF INVESTIGATION
#5: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Mg / タイプ: SUBJECT OF INVESTIGATION
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 5 / 由来タイプ: 天然 / 式: H2O

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詳細

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: 2.38 Å3/Da / 溶媒含有率: 48.39 %
結晶化温度: 293 K / 手法: 蒸発脱水法 / 詳細: Tris-HCl, MgCl2, PEG 3350

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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: SSRF / ビームライン: BL17U1 / 波長: 0.9791 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2018年5月28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: 0.9791 Å / 相対比: 1
反射解像度: 2.849→50 Å / Num. obs: 60768 / % possible obs: 96.11 % / 冗長度: 6.2 % / Rsym value: 0.157 / Net I/σ(I): 17.9
反射 シェル解像度: 2.85→2.96 Å / Num. unique obs: 5694 / Rsym value: 0.75

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解析

ソフトウェア
名称バージョン分類
PHENIXdev_2666精密化
PDB_EXTRACT3.25データ抽出
HKL-2000データ削減
HKL-2000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: 1JSC, 2LVW

1jsc

2lvw


解像度: 2.849→35.929 Å / SU ML: 0.34 / 交差検証法: THROUGHOUT / σ(F): 0 / 位相誤差: 24.56
Rfactor反射数%反射
Rfree0.2433 1947 3.31 %
Rwork0.1673 --
obs0.1697 58894 96.17 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 170.2 Å2 / Biso mean: 63.9853 Å2 / Biso min: 17.96 Å2
精密化ステップサイクル: final / 解像度: 2.849→35.929 Å
タンパク質核酸リガンド溶媒全体
原子数18515 0 320 5 18840
Biso mean--55.75 41.45 -
残基数----2486
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00919215
X-RAY DIFFRACTIONf_angle_d1.30226221
X-RAY DIFFRACTIONf_chiral_restr0.073051
X-RAY DIFFRACTIONf_plane_restr0.0093387
X-RAY DIFFRACTIONf_dihedral_angle_d7.611456
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A9117X-RAY DIFFRACTION13.944TORSIONAL
12B9117X-RAY DIFFRACTION13.944TORSIONAL
13C9117X-RAY DIFFRACTION13.944TORSIONAL
14D9117X-RAY DIFFRACTION13.944TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8494-2.92070.30511140.2293341081
2.9207-2.99960.32561260.2245386391
2.9996-3.08780.32931390.2116386392
3.0878-3.18740.29921310.1956394294
3.1874-3.30130.23811410.1877405496
3.3013-3.43330.25251310.181410797
3.4333-3.58950.29261560.1821415098
3.5895-3.77850.25761270.1617413999
3.7785-4.0150.22071520.1529419099
4.015-4.32450.21791400.14424207100
4.3245-4.75880.20671460.13514215100
4.7588-5.44530.21971480.14844263100
5.4453-6.85280.27661460.19064241100
6.8528-35.9290.20931500.1621430399
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)
15.6586-0.88993.92643.465-4.86568.75150.08890.46650.0406-0.3704-0.0856-0.31080.3815-0.3148-0.07240.3305-0.0750.01530.22160.00560.341913.001-12.99634.0674
26.75482.67614.24886.2592-0.64513.7869-0.4081-0.59660.03590.0962-0.08820.1293-0.3347-0.24290.54930.27520.010.10350.47560.00490.25069.6242-12.681514.0059
39.11840.9546-7.1882.1371.61588.6244-0.0453-1.0076-1.52010.4347-0.679-0.86870.32991.05860.54040.4098-0.00660.01840.72590.2040.359720.1431-13.934315.4966
42.11862.08611.93879.02794.26732.61270.0130.74820.9204-1.4066-0.44130.5043-0.0057-1.00350.47360.42080.0526-0.04860.89780.13780.355411.7095-6.3214-2.5313
56.30444.0585-4.62649.1813-1.04595.2015-0.03060.9381-0.36460.148-0.6937-1.14490.03890.51610.01650.30280.02020.06910.51780.05910.391118.6035-15.43436.6247
69.37096.5963-5.65998.2112-1.40015.9671-0.11880.3346-0.5419-0.0484-0.0393-0.16060.027-0.16980.32030.31780.0418-0.03980.3662-0.00650.402413.4137-20.2086.13
74.629-2.31223.55682.4284-3.35486.06160.3304-0.0623-0.2519-1.4655-0.89-0.5339-0.46770.04270.51270.4335-0.02370.08430.51720.04610.475327.981-3.99033.902
82.0758-1.0917-0.45741.6722-0.36771.6392-0.01320.1746-0.1726-0.36530.11120.7887-0.019-0.2978-0.05430.3339-0.033-0.14480.39680.14690.6989-17.2283-15.194315.9672
93.973-2.25390.92913.28130.12232.5737-0.00170.639-0.0893-0.42330.03420.3673-0.30270.1990.04540.2917-0.0985-0.11050.50220.1640.4739-8.3987-10.71398.6484
102.0353-3.21490.74754.9359-1.34790.08670.41720.9365-0.5901-0.8811-0.44780.6040.2130.07240.05130.53280.0671-0.1250.6296-0.17850.83920.9694-38.77865.1115
112.5948-0.6345-1.36152.8251-0.10672.4568-0.1506-0.054-0.72780.30370.07850.67470.1553-0.05120.08870.2448-0.01060.01930.34090.1310.67433.4781-43.138125.28
122.7635-0.6319-0.73122.17-0.77330.4739-0.1035-0.2284-0.98940.07440.1230.48960.2744-0.13050.02010.4307-0.0301-0.01050.4040.08430.72881.1744-44.882725.0124
132.9648-0.12420.6162.71850.86981.2482-0.0627-0.5732-0.42110.38860.1340.77910.1168-0.1192-0.07770.38210.06250.14890.47380.23640.6391-12.4963-27.163236.3603
141.0564-1.30420.39371.80510.74041.81120.0636-0.6077-0.24010.11430.20010.33730.0807-0.0523-0.26220.45090.06980.18790.72810.35010.8475-15.1785-30.77643.2105
156.7246-2.4209-3.41188.52145.4824.4848-0.11140.49410.13020.0212-0.14320.1172-0.3773-0.19860.40010.44920.05530.03550.54020.15580.275638.18684.4798-20.1043
166.59341.3912.27444.07620.33841.73230.16040.19550.2696-0.2185-0.01010.2132-0.60780.3402-0.03540.4505-0.07360.03210.45830.07130.206748.73764.9307-20.2951
176.2771.4997-2.0323.3371-1.97823.1692-0.9135-0.23980.1669-1.08060.5009-0.0403-1.40050.6930.24580.6614-0.16380.02360.72060.00820.256943.83366.466-13.7256
181.99522.34776.02127.87183.4959.80240.19290.0632-2.3994-0.51760.8335-0.10961.2127-3.2461-0.84940.4798-0.10920.04361.12040.28010.609929.8066-4.8876-24.1696
197.7093-1.14932.13557.08272.85318.1266-0.80840.7229-0.28690.20480.91490.6072-0.8707-1.2401-0.30550.4745-0.07790.03030.59770.15310.276536.82314.622-16.5457
205.7389-5.4165-2.91665.4223.91325.8492-0.22930.40172.20361.16381.6996-0.9324-3.70310.6417-1.10641.2458-0.11910.07390.5336-0.05431.15143.246620.036-11.1256
219.15720.0105-3.83295.61654.57925.7879-0.3836-0.03491.211-2.36330.45080.2881-1.60230.41760.11560.9941-0.0844-0.07860.43870.15830.430943.503813.6257-23.5819
228.8876-0.8405-6.55662.29750.05844.9490.21760.83880.53670.26120.31290.6427-0.0818-0.8541-0.43520.54440.07970.08590.61120.13930.482633.099910.9422-17.1999
231.8918-1.972-0.36242.44370.55920.1543-0.0371-0.29780.31570.59511.33850.5456-1.1346-0.3766-1.06750.68950.01010.21670.80610.12090.412435.6540.9104-2.2111
242.00310.71830.16072.0850.80461.2022-0.25670.51380.0088-0.41760.37930.17070.3202-0.3478-0.09440.4739-0.176-0.02280.62320.01250.207655.6351-2.5408-41.9016
252.19380.28070.30413.54590.33562.134-0.15020.15910.3502-0.03660.23090.7756-0.0239-0.95850.00710.3692-0.099-0.00160.8410.05110.413644.23177.6192-40.7969
263.7908-0.30260.51372.91581.26741.3804-0.34070.36031.408-0.47120.08750.1579-0.5276-0.24090.17170.5117-0.0215-0.13940.55420.17390.776162.493629.0442-40.2061
272.45410.07740.07672.74010.0163.216-0.16970.44150.5714-0.30910.28-0.5351-0.50890.4273-0.03790.4212-0.14150.06950.58050.06240.540581.383214.414-41.359
287.6712-4.66593.45918.6897-2.75915.2609-0.62620.53070.55960.105-0.233-0.7852-0.0675-0.61520.60320.3174-0.13280.13720.45480.07320.492317.93362.418514.0484
292.5632.16130.66946.0576-0.24628.50560.26520.66361.31350.7922-0.01680.5342-0.4572-0.2493-0.0880.3985-0.05220.08380.29910.11010.38637.6208-0.749314.8929
303.05550.4559-2.70334.16180.792.7449-0.27830.66810.8716-0.39070.0697-0.0306-0.5479-0.676-0.20260.47310.09290.0070.52140.16890.411113.35310.13767.0831
314.75871.7799-1.2226.09840.55426.91890.15450.28871.1367-0.04570.0153-0.0411-0.3576-0.619-0.16970.3446-0.04790.08190.43570.10210.524816.15366.844212.8364
326.1740.5529-5.43067.72552.66366.0584-0.63680.3936-0.3965-0.47451.0772-0.1464-0.8491-1.2021-0.27240.55260.1056-0.02210.79390.05290.339721.7798-1.3627-3.0216
332.3764-0.43940.52952.2482-0.80542.2015-0.0066-0.56590.14240.30590.0740.0920.03660.164-0.0740.30690.02390.01810.53050.03040.23075.8573-6.312237.1017
341.3941-0.1623-0.40761.87210.17890.6784-0.0896-0.1250.8374-0.02710.24640.303-0.20860.0235-0.14350.4789-0.00140.07060.44820.0420.9089-10.593216.104732.8512
351.9709-1.01940.70032.2199-0.7245.5591-0.1473-0.0930.32820.13530.08240.6118-0.5007-0.45360.03070.45230.04120.06720.48640.09820.9713-27.92330.538632.751
365.93414.3921-1.0363.8275-0.68285.87980.43930.0547-0.02121.04720.22710.3488-0.16540.2145-0.53930.4665-0.00610.10650.47340.04750.406948.883-5.3571-7.632
373.8547-0.67783.12346.95465.18167.366-0.65920.490.2307-0.04860.1977-0.12440.2072-0.44920.31540.4858-0.06980.18410.49270.19960.352151.6505-4.8174-17.1996
387.8407-5.3921-7.65657.94685.54917.4795-0.5260.2497-0.2851-0.73480.71250.02120.23070.6118-0.27070.6956-0.18060.09020.52-0.00210.246844.1593-7.1691-14.672
395.70116.05746.07476.56046.41316.5060.6718-0.7915-0.30321.6978-0.6172-0.04771.1424-0.16850.25780.6486-0.11530.080.5041-0.00060.378945.6073-5.6676-5.8103
404.36353.7578-1.84424.2567-0.37776.8079-0.93620.1663-0.8296-0.98660.27090.5517-0.21670.22550.50070.6533-0.00090.08440.47970.01330.439751.4994-17.2546-13.7384
414.41215.6932-4.67668.4186-5.10435.7898-0.3362-0.9234-0.7552-0.1593-0.2157-0.22070.66620.22030.45190.57960.00470.02950.43950.07210.400448.6688-10.9045-5.3455
424.903-4.29882.10424.2903-3.07183.7147-0.2230.9212-0.66580.4056-0.02460.93770.1621-0.58250.18960.3657-0.02990.10980.57920.03420.520330.8094-4.4558-9.0945
431.91430.6552-0.15023.13481.24853.22480.0048-0.4246-0.0150.27370.0821-0.51540.250.1707-0.08450.23960.0121-0.05370.3369-0.01380.302178.56251.5411-19.7032
443.19672.21851.20954.9601-0.35722.0690.0836-0.41120.28660.4912-0.170.1157-0.1717-0.25910.05870.3160.03880.04680.4146-0.03710.195567.99242.9473-13.9799
451.5508-0.5526-0.38054.41681.6743.1064-0.1625-0.1305-0.7662-0.07130.0239-0.13590.9381-0.01320.16640.71990.00330.11130.38320.09670.636771.7407-31.6448-19.0682
465.2343-0.29442.110.11550.58215.8338-0.1474-0.1151-0.0915-0.1068-0.0156-0.14720.3967-0.370.14180.8388-0.10070.02860.35010.10610.481762.7848-29.7993-17.5002
471.6329-0.2383-0.73052.4965-0.17581.3679-0.29930.5777-0.6476-0.61460.1046-0.70770.70260.0540.04930.7234-0.05220.2010.4184-0.15750.487578.443-19.2805-36.525
480.21191.2540.69155.03852.53822.0368-0.21250.6156-0.3819-0.25080.1837-0.190.1395-0.12120.01840.7192-0.01330.2020.7205-0.22840.670282.8623-17.735-43.889
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 7 through 20 )E7 - 20
2X-RAY DIFFRACTION2chain 'E' and (resid 21 through 32 )E21 - 32
3X-RAY DIFFRACTION3chain 'E' and (resid 33 through 38 )E33 - 38
4X-RAY DIFFRACTION4chain 'E' and (resid 39 through 48 )E39 - 48
5X-RAY DIFFRACTION5chain 'E' and (resid 49 through 61 )E49 - 61
6X-RAY DIFFRACTION6chain 'E' and (resid 62 through 84 )E62 - 84
7X-RAY DIFFRACTION7chain 'E' and (resid 85 through 95 )E85 - 95
8X-RAY DIFFRACTION8chain 'A' and (resid 11 through 111 )A11 - 111
9X-RAY DIFFRACTION9chain 'A' and (resid 112 through 180 )A112 - 180
10X-RAY DIFFRACTION10chain 'A' and (resid 181 through 209 )A181 - 209
11X-RAY DIFFRACTION11chain 'A' and (resid 210 through 307 )A210 - 307
12X-RAY DIFFRACTION12chain 'A' and (resid 308 through 380 )A308 - 380
13X-RAY DIFFRACTION13chain 'A' and (resid 381 through 499 )A381 - 499
14X-RAY DIFFRACTION14chain 'A' and (resid 500 through 560 )A500 - 560
15X-RAY DIFFRACTION15chain 'F' and (resid 8 through 20 )F8 - 20
16X-RAY DIFFRACTION16chain 'F' and (resid 21 through 31 )F21 - 31
17X-RAY DIFFRACTION17chain 'F' and (resid 32 through 43 )F32 - 43
18X-RAY DIFFRACTION18chain 'F' and (resid 44 through 48 )F44 - 48
19X-RAY DIFFRACTION19chain 'F' and (resid 49 through 56 )F49 - 56
20X-RAY DIFFRACTION20chain 'F' and (resid 57 through 61 )F57 - 61
21X-RAY DIFFRACTION21chain 'F' and (resid 62 through 74 )F62 - 74
22X-RAY DIFFRACTION22chain 'F' and (resid 75 through 84 )F75 - 84
23X-RAY DIFFRACTION23chain 'F' and (resid 85 through 96 )F85 - 96
24X-RAY DIFFRACTION24chain 'B' and (resid 8 through 143 )B8 - 143
25X-RAY DIFFRACTION25chain 'B' and (resid 144 through 209 )B144 - 209
26X-RAY DIFFRACTION26chain 'B' and (resid 210 through 437 )B210 - 437
27X-RAY DIFFRACTION27chain 'B' and (resid 438 through 560 )B438 - 560
28X-RAY DIFFRACTION28chain 'G' and (resid 8 through 20 )G8 - 20
29X-RAY DIFFRACTION29chain 'G' and (resid 21 through 32 )G21 - 32
30X-RAY DIFFRACTION30chain 'G' and (resid 33 through 43 )G33 - 43
31X-RAY DIFFRACTION31chain 'G' and (resid 44 through 84 )G44 - 84
32X-RAY DIFFRACTION32chain 'G' and (resid 85 through 95 )G85 - 95
33X-RAY DIFFRACTION33chain 'C' and (resid 11 through 176 )C11 - 176
34X-RAY DIFFRACTION34chain 'C' and (resid 177 through 470 )C177 - 470
35X-RAY DIFFRACTION35chain 'C' and (resid 471 through 560 )C471 - 560
36X-RAY DIFFRACTION36chain 'H' and (resid 8 through 20 )H8 - 20
37X-RAY DIFFRACTION37chain 'H' and (resid 21 through 31 )H21 - 31
38X-RAY DIFFRACTION38chain 'H' and (resid 32 through 43 )H32 - 43
39X-RAY DIFFRACTION39chain 'H' and (resid 44 through 59 )H44 - 59
40X-RAY DIFFRACTION40chain 'H' and (resid 60 through 71 )H60 - 71
41X-RAY DIFFRACTION41chain 'H' and (resid 72 through 84 )H72 - 84
42X-RAY DIFFRACTION42chain 'H' and (resid 85 through 95 )H85 - 95
43X-RAY DIFFRACTION43chain 'D' and (resid 11 through 101 )D11 - 101
44X-RAY DIFFRACTION44chain 'D' and (resid 102 through 180 )D102 - 180
45X-RAY DIFFRACTION45chain 'D' and (resid 181 through 275 )D181 - 275
46X-RAY DIFFRACTION46chain 'D' and (resid 276 through 337 )D276 - 337
47X-RAY DIFFRACTION47chain 'D' and (resid 338 through 499 )D338 - 499
48X-RAY DIFFRACTION48chain 'D' and (resid 500 through 560 )D500 - 560

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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://pdbjlc1.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