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- PDB-5vbf: Crystal structure of succinate semialdehyde dehydrogenase from Bu... -

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基本情報

登録情報
データベース: PDB / ID: 5vbf
タイトルCrystal structure of succinate semialdehyde dehydrogenase from Burkholderia vietnamiensis
要素NAD-dependent succinate-semialdehyde dehydrogenase
キーワードOXIDOREDUCTASE / SSGCID / succinate semialdehyde dehydrogenase / Burkholderia vietnamiensis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
機能・相同性
機能・相同性情報


succinate-semialdehyde dehydrogenase [NAD(P)+] / succinate-semialdehyde dehydrogenase [NAD(P)+] activity / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
類似検索 - 分子機能
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
FORMIC ACID / NAD-dependent succinate-semialdehyde dehydrogenase / Succinate semialdehyde dehydrogenase
類似検索 - 構成要素
生物種Burkholderia vietnamiensis (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.35 Å
データ登録者Seattle Structural Genomics Center for Infectious Disease (SSGCID)
引用ジャーナル: to be published
タイトル: Crystal structure of succinate semialdehyde dehydrogenase from Burkholderia vietnamiensis
著者: Conrady, D.G. / Fox III, D. / Lorimer, D.D. / Edwards, T.E.
履歴
登録2017年3月29日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年4月12日Provider: repository / タイプ: Initial release
改定 1.12023年10月4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
A: NAD-dependent succinate-semialdehyde dehydrogenase
B: NAD-dependent succinate-semialdehyde dehydrogenase
C: NAD-dependent succinate-semialdehyde dehydrogenase
D: NAD-dependent succinate-semialdehyde dehydrogenase
E: NAD-dependent succinate-semialdehyde dehydrogenase
F: NAD-dependent succinate-semialdehyde dehydrogenase
G: NAD-dependent succinate-semialdehyde dehydrogenase
H: NAD-dependent succinate-semialdehyde dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)413,46336
ポリマ－410,9808
非ポリマー2,48328
水52,6042920
1
A: NAD-dependent succinate-semialdehyde dehydrogenase
B: NAD-dependent succinate-semialdehyde dehydrogenase
C: NAD-dependent succinate-semialdehyde dehydrogenase
D: NAD-dependent succinate-semialdehyde dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)206,73218
ポリマ－205,4904
非ポリマー1,24114
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area20770 Å2
ΔGint-59 kcal/mol
Surface area57660 Å2
手法PISA
2
E: NAD-dependent succinate-semialdehyde dehydrogenase
F: NAD-dependent succinate-semialdehyde dehydrogenase
G: NAD-dependent succinate-semialdehyde dehydrogenase
H: NAD-dependent succinate-semialdehyde dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)206,73218
ポリマ－205,4904
非ポリマー1,24114
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area20850 Å2
ΔGint-58 kcal/mol
Surface area56910 Å2
手法PISA
単位格子
Length a, b, c (Å)106.620, 191.760, 219.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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
11(chain A and ((resid 8 and (name N or name...
21(chain B and ((resid 8 and (name N or name...
31(chain C and (resid 8 through 12 or resid 14...
41(chain D and (resid 8 through 12 or resid 14...
51(chain E and (resid 8 through 12 or resid 14...
61(chain F and (resid 8 through 12 or resid 14...
71(chain G and ((resid 8 and (name N or name...
81(chain H and ((resid 8 and (name N or name...

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
11ASPASPASPASP(chain A and ((resid 8 and (name N or name...AA83
12ARGARGASNASN(chain A and ((resid 8 and (name N or name...AA6 - 4831 - 478
13ARGARGASNASN(chain A and ((resid 8 and (name N or name...AA6 - 4831 - 478
14ARGARGASNASN(chain A and ((resid 8 and (name N or name...AA6 - 4831 - 478
15ARGARGASNASN(chain A and ((resid 8 and (name N or name...AA6 - 4831 - 478
21ASPASPASPASP(chain B and ((resid 8 and (name N or name...BB83
22ARGARGASNASN(chain B and ((resid 8 and (name N or name...BB6 - 4831 - 478
23ARGARGASNASN(chain B and ((resid 8 and (name N or name...BB6 - 4831 - 478
24ARGARGASNASN(chain B and ((resid 8 and (name N or name...BB6 - 4831 - 478
25ARGARGASNASN(chain B and ((resid 8 and (name N or name...BB6 - 4831 - 478
31ASPASPLEULEU(chain C and (resid 8 through 12 or resid 14...CC8 - 123 - 7
32LEULEUGLYGLY(chain C and (resid 8 through 12 or resid 14...CC14 - 189 - 13
33ARGARGARGARG(chain C and (resid 8 through 12 or resid 14...CC1914
34ASPASPASNASN(chain C and (resid 8 through 12 or resid 14...CC8 - 4833 - 478
35ASPASPASNASN(chain C and (resid 8 through 12 or resid 14...CC8 - 4833 - 478
36ASPASPASNASN(chain C and (resid 8 through 12 or resid 14...CC8 - 4833 - 478
37ASPASPASNASN(chain C and (resid 8 through 12 or resid 14...CC8 - 4833 - 478
41ASPASPLEULEU(chain D and (resid 8 through 12 or resid 14...DD8 - 123 - 7
42LEULEUHISHIS(chain D and (resid 8 through 12 or resid 14...DD14 - 219 - 16
43ALAALAASPASP(chain D and (resid 8 through 12 or resid 14...DD23 - 2418 - 19
44HISHISASNASN(chain D and (resid 8 through 12 or resid 14...DD7 - 4832 - 478
45HISHISASNASN(chain D and (resid 8 through 12 or resid 14...DD7 - 4832 - 478
46HISHISASNASN(chain D and (resid 8 through 12 or resid 14...DD7 - 4832 - 478
47HISHISASNASN(chain D and (resid 8 through 12 or resid 14...DD7 - 4832 - 478
51ASPASPLEULEU(chain E and (resid 8 through 12 or resid 14...EE8 - 123 - 7
52LEULEUHISHIS(chain E and (resid 8 through 12 or resid 14...EE14 - 219 - 16
53ALAALAASPASP(chain E and (resid 8 through 12 or resid 14...EE23 - 2418 - 19
54ASPASPASNASN(chain E and (resid 8 through 12 or resid 14...EE8 - 4833 - 478
55ASPASPASNASN(chain E and (resid 8 through 12 or resid 14...EE8 - 4833 - 478
56ASPASPASNASN(chain E and (resid 8 through 12 or resid 14...EE8 - 4833 - 478
57ASPASPASNASN(chain E and (resid 8 through 12 or resid 14...EE8 - 4833 - 478
61ASPASPLEULEU(chain F and (resid 8 through 12 or resid 14...FF8 - 123 - 7
62LEULEUHISHIS(chain F and (resid 8 through 12 or resid 14...FF14 - 219 - 16
63ALAALAASPASP(chain F and (resid 8 through 12 or resid 14...FF23 - 2418 - 19
64ASPASPASNASN(chain F and (resid 8 through 12 or resid 14...FF8 - 4833 - 478
65ASPASPASNASN(chain F and (resid 8 through 12 or resid 14...FF8 - 4833 - 478
66ASPASPASNASN(chain F and (resid 8 through 12 or resid 14...FF8 - 4833 - 478
67ASPASPASNASN(chain F and (resid 8 through 12 or resid 14...FF8 - 4833 - 478
71ASPASPASPASP(chain G and ((resid 8 and (name N or name...GG83
72HISHISASNASN(chain G and ((resid 8 and (name N or name...GG7 - 4832 - 478
73HISHISASNASN(chain G and ((resid 8 and (name N or name...GG7 - 4832 - 478
74HISHISASNASN(chain G and ((resid 8 and (name N or name...GG7 - 4832 - 478
75HISHISASNASN(chain G and ((resid 8 and (name N or name...GG7 - 4832 - 478
81ASPASPASPASP(chain H and ((resid 8 and (name N or name...HH83
82HISHISASNASN(chain H and ((resid 8 and (name N or name...HH7 - 4832 - 478
83HISHISASNASN(chain H and ((resid 8 and (name N or name...HH7 - 4832 - 478
84HISHISASNASN(chain H and ((resid 8 and (name N or name...HH7 - 4832 - 478
85HISHISASNASN(chain H and ((resid 8 and (name N or name...HH7 - 4832 - 478

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要素

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タンパク質 , 1種, 8分子 ABCDEFGH

#1: タンパク質
NAD-dependent succinate-semialdehyde dehydrogenase


分子量: 51372.559 Da / 分子数: 8 / 断片: BuviA.00020.v.B1 / 由来タイプ: 組換発現
由来: (組換発現) Burkholderia vietnamiensis (バクテリア)
遺伝子: WK24_04400 / プラスミド: BuviA.00104.b.B2 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: A0A132DEP7, UniProt: A4JQH6*PLUS

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非ポリマー , 5種, 2948分子

#2: 化合物
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / 2-モルホリノエタンスルホン酸


分子量: 195.237 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C6H13NO4S / コメント: pH緩衝剤*YM
#3: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C3H8O3
#4: 化合物
ChemComp-FMT / FORMIC ACID / ギ酸


分子量: 46.025 Da / 分子数: 4 / 由来タイプ: 合成 / 式: CH2O2
#5: 化合物
ChemComp-UNX / UNKNOWN ATOM OR ION


分子数: 8 / 由来タイプ: 合成
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2920 / 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: 2.73 Å3/Da / 溶媒含有率: 55.01 %
結晶化温度: 290 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5
詳細: Rigaku Reagents Morpheus Screen G3: 0.020M Sodium Formate, 0.020M Ammonium Acetate, 0.020M Sodium Citrate, 0.020M Sodium Tartrate, 0.020M Sodium Oxamate, 0.1 M Imidazole/MES pH 6.5, 20% ...詳細: Rigaku Reagents Morpheus Screen G3: 0.020M Sodium Formate, 0.020M Ammonium Acetate, 0.020M Sodium Citrate, 0.020M Sodium Tartrate, 0.020M Sodium Oxamate, 0.1 M Imidazole/MES pH 6.5, 20% glycerol, 10% PEG 4000: BuviA.00020.v.B1.PS02593 at 14 mg/ml

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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: シンクロトロン / サイト: APS / ビームライン: 21-ID-F / 波長: 0.97872 Å
検出器タイプ: RAYONIX MX-300 / 検出器: CCD / 日付: 2016年6月22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: 0.97872 Å / 相対比: 1
反射解像度: 2.35→48.166 Å / Num. obs: 184886 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / 冗長度: 6.379 % / Biso Wilson estimate: 16.72 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.158 / Rrim(I) all: 0.172 / Χ2: 0.933 / Net I/σ(I): 10.69
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.416.3350.5173.93137070.8690.56499.7
2.41-2.486.3510.4794.23133130.880.52299.8
2.48-2.556.360.4164.76130010.9080.45399.7
2.55-2.636.370.3715.25126000.9280.40499.6
2.63-2.716.3560.3086.23122240.9470.33599.5
2.71-2.816.3640.2726.94118270.9580.29699.4
2.81-2.916.3930.2447.65113450.9660.26599.2
2.91-3.036.3760.2198.47109770.9710.23899.1
3.03-3.176.4020.18110.01104780.980.19798.8
3.17-3.326.3810.15311.49100270.9860.16698.7
3.32-3.56.4160.12413.7794830.990.13498.5
3.5-3.726.40.1115.0890520.9920.1298.5
3.72-3.976.4140.09417.1284970.9930.10398.3
3.97-4.296.4140.08418.8778950.9940.09197.9
4.29-4.76.4350.07420.6472610.9950.08197.8
4.7-5.256.4170.07719.9165710.9950.08497.6
5.25-6.076.4410.08817.6658090.9940.09596.9
6.07-7.436.4180.08118.7948990.9950.08896.2
7.43-10.516.3450.06224.4138180.9970.06794.9
10.51-48.16660.06323.7621020.9950.06990.6

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類NB
XSCALEデータスケーリング
PHENIXdev_2689精密化
PDB_EXTRACT3.22データ抽出
XDSデータ削減
MoRDa位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3JZ4

3jz4


解像度: 2.35→48.166 Å / SU ML: 0.23 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 18.59
Rfactor反射数%反射
Rfree0.196 1984 1.07 %
Rwork0.1471 --
obs0.1476 184837 98.66 %
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: 106.78 Å2 / Biso mean: 19.9614 Å2 / Biso min: 1.48 Å2
精密化ステップサイクル: final / 解像度: 2.35→48.166 Å
タンパク質核酸リガンド溶媒全体
原子数28535 0 164 2923 31622
Biso mean--41.89 25.87 -
残基数----3815
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00729668
X-RAY DIFFRACTIONf_angle_d0.84640400
X-RAY DIFFRACTIONf_chiral_restr0.0524471
X-RAY DIFFRACTIONf_plane_restr0.0065377
X-RAY DIFFRACTIONf_dihedral_angle_d13.93317792
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A16492X-RAY DIFFRACTION7.102TORSIONAL
12B16492X-RAY DIFFRACTION7.102TORSIONAL
13C16492X-RAY DIFFRACTION7.102TORSIONAL
14D16492X-RAY DIFFRACTION7.102TORSIONAL
15E16492X-RAY DIFFRACTION7.102TORSIONAL
16F16492X-RAY DIFFRACTION7.102TORSIONAL
17G16492X-RAY DIFFRACTION7.102TORSIONAL
18H16492X-RAY DIFFRACTION7.102TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3499-2.40870.24481420.18411305313195100
2.4087-2.47380.23971490.17721308313232100
2.4738-2.54660.22091520.16981306013212100
2.5466-2.62880.23121510.16691305413205100
2.6288-2.72270.23581290.1606130701319999
2.7227-2.83170.23041360.1625130451318199
2.8317-2.96060.21111210.1607131211324299
2.9606-3.11670.21561560.1591130041316099
3.1167-3.31190.19281340.1526130511318599
3.3119-3.56750.18871460.1397130061315298
3.5675-3.92640.17331390.1356131041324398
3.9264-4.49420.1631290.1149130261315598
4.4942-5.66080.14971510.1195130561320797
5.6608-48.17610.17551490.1444131201326995
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)
11.5897-0.133-0.01231.09660.23150.51910.0516-0.15110.23590.049-0.01680.036-0.17880.0482-0.06070.1844-0.0240.00910.1078-0.03590.136919.891719.2493-14.8224
20.1153-0.0510.02370.33280.15090.22380.0192-0.0330.02630.0507-0.01290.0387-0.0195-0.0403-0.01160.138-0.00720.01510.1202-0.00690.106812.96091.4667-19.8659
31.79590.32231.3981.34440.7633.63630.0209-0.01530.187-0.0267-0.10780.1811-0.2477-0.21810.10370.15260.03150.05450.1576-0.03090.1734-10.76427.3432-16.3592
41.84930.2056-0.36580.2204-0.03920.2113-0.0019-0.02570.01030.0294-0.00970.04580.0026-0.01820.01710.1226-0.00840.00580.1261-0.0150.10295.1799-9.655-28.5821
50.95870.0810.08931.1942-0.63891.1707-0.04150.1076-0.0063-0.11490.02930.03390.0102-0.05770.0110.0872-0.0176-0.01520.1081-0.0340.075811.247-9.81-62.9
60.20030.02480.05780.24010.00050.21010.00480.00090.00870.0048-0.0238-0.0073-0.0035-0.02960.01470.09760.0003-0.0020.11610.00070.105218.9193-6.462-49.8733
71.7550.78580.71231.38350.41562.0755-0.04060.08010.0999-0.0531-0.0150.0066-0.1176-0.01220.05670.0803-0.00280.03080.11090.03490.107740.35877.8989-61.0726
81.30910.2776-0.53360.08490.01720.6503-0.01290.0436-0.03710.01770.02550.0110.00760.0115-0.01310.1202-0.0051-0.01050.09510.00640.089831.4296-3.6764-39.9191
90.57220.44780.0192.0146-0.10280.2218-0.00370.0211-0.0786-0.07450.0414-0.1540.00670.0241-0.03960.1195-0.00180.04130.1003-0.01980.078630.8108-48.1914-48.3233
100.32620.29970.07930.78380.27150.08120.0327-0.0229-0.06560.0389-0.0132-0.10940.01250.0182-0.02180.11410.00640.01010.09990.01090.116730.4416-38.7247-39.2844
112.0608-0.64070.06430.2489-0.11020.1494-0.0175-0.1690.10510.03750.0459-0.01550.002-0.0057-0.02020.155-0.01820.00680.1067-0.00830.145414.9445-45.0117-27.9329
121.0720.0153-0.44071.06130.59862.55640.0303-0.1048-0.15360.1358-0.03370.06940.23440.0259-0.00120.1139-0.0089-0.0010.09390.040.14633.5576-56.042-28.1899
132.80860.387-0.02041.1297-0.26941.0141-0.1069-0.1346-0.04260.2425-0.03480.04480.0529-0.00640.09280.15590.00760.01290.1399-0.01440.0746.9316-37.2918-19.3293
142.24511.095-0.03420.57080.08070.1691-0.0278-0.0295-0.1355-0.0361-0.0281-0.0366-0.05510.02950.0640.1685-0.00780.00980.11120.00550.090125.6089-30.8002-30.3791
151.2697-0.14350.38210.5738-0.25950.53880.0465-0.2453-0.11180.1515-0.0269-0.02750.0521-0.0951-0.01740.2218-0.01390.00020.19390.02220.079934.7199-26.96833.0342
160.1434-0.11990.00910.07820.01720.1743-0.0206-0.0638-0.04960.0580.0269-0.01260.06110.024-0.00890.1869-0.0048-0.01160.16040.01870.120736.0494-27.1142-12.2793
171.0174-0.0604-0.47960.65990.11972.82690.003-0.0811-0.08960.15760.0185-0.17370.21670.3013-0.01030.15520.0277-0.06010.18530.01310.156863.9064-25.2956-14.6604
182.16630.5361-0.37360.20630.13020.099-0.0069-0.0272-0.07260.03040.02340.00850.0380.0055-0.01630.14760.0178-0.00180.12370.01240.086541.4768-24.0152-27.2375
191.1412-0.0511-0.01870.9693-0.39360.8232-0.0512-0.20210.00620.19810.10220.0839-0.0134-0.0544-0.05080.17190.04860.03430.1663-0.01170.0989-38.5246-32.2627-49.9827
200.2479-0.0760.03120.3741-0.0110.5512-0.0364-0.0361-0.00670.04980.06020.04160.058-0.0183-0.03010.13120.00650.00890.12080.01350.1294-36.8108-31.8339-62.8774
212.89010.44730.03840.49760.10590.1617-0.0362-0.0470.0416-0.01690.0262-0.04260.14690.0097-0.01030.19320.0138-0.0130.17610.00930.1343-26.3296-44.9598-68.8089
221.49370.818-0.42290.8992-0.30540.6453-0.0030.0310.10750.15440.0669-0.15820.08130.0827-0.02480.16530.0454-0.0760.17560.00730.1672-10.0544-38.9827-58.2151
231.4841-1.0162-0.7632.44792.59646.4409-0.024-0.1629-0.0440.10570.056-0.18890.11210.3415-0.03660.12170.0315-0.03840.08540.02270.2209-0.4249-44.9398-61.3185
242.2257-0.6988-0.69142.95520.95731.9427-0.0679-0.2082-0.05830.28970.06520.10960.0816-0.16760.01010.20570.0623-0.05340.18840.03310.1177-15.6942-48.4992-48.1447
252.421-0.4273-0.461.7651-0.05881.4385-0.0949-0.2203-0.27190.0830.0497-0.07790.20440.03230.01270.1720.0462-0.04430.12340.02690.1485-9.6169-52.4288-56.6441
262.29720.38390.17791.0669-0.15640.89980.0113-0.0313-0.18130.03990.0076-0.13490.17620.1195-0.03440.16430.0328-0.02130.1171-0.01860.1186-10.1891-41.9377-75.0772
272.003-0.13920.68890.19080.15080.4499-0.0632-0.02190.06060.05970.00210.0248-0.02470.06570.05740.1450.0168-0.00890.1371-0.00820.136-30.4334-31.5634-74.0522
281.4473-0.2184-0.11441.17160.03970.19620.03220.1326-0.1812-0.2394-0.01770.07230.0883-0.0922-0.02060.2727-0.0277-0.04590.125-0.02250.1271-33.3937-52.0592-101.8998
290.28880.0598-0.02260.64130.10690.2376-0.00630.0052-0.0671-0.07990.02550.04930.097-0.0622-0.02360.165-0.0089-0.02950.1054-0.00370.1548-31.8478-43.6204-91.9928
303.2613-2.98031.35283.2318-1.52960.9166-0.0988-0.02270.35330.0397-0.0142-0.11360.03050.02130.1140.1766-0.0296-0.04790.1504-0.02380.1838-46.41-42.1441-82.0774
311.2061-0.0788-0.09531.29120.77471.35260.06070.1356-0.1631-0.1007-0.01870.43690.1221-0.13810.01770.1923-0.0607-0.13120.21480.01660.3711-62.5795-39.3806-96.6434
322.03-0.0951-0.15211.09140.33751.7483-0.08580.072-0.28-0.0191-0.13520.64370.203-0.2120.03850.2304-0.0901-0.0970.19280.00930.5208-66.2974-45.8445-92.5227
331.4248-0.24220.14161.5680.10481.0581-0.0179-0.0726-0.06450.08170.04150.32440.1152-0.1383-0.00460.1589-0.0151-0.03550.130.01290.2112-58.2348-27.9932-82.48
341.4484-0.90070.4730.5739-0.44040.39890.0370.029-0.0569-0.07990.00410.06990.01480.0685-0.03360.1732-0.02130.00180.1022-0.02120.1622-34.4968-33.5952-84.3749
351.3170.18630.1840.9111-0.00210.42560.00520.24470.0441-0.24070.0238-0.0333-0.02450.0281-0.02960.201-0.004-0.00010.14590.02670.0921-20.702-10.8444-116.4514
360.33420.0568-0.09220.26890.03940.357-0.0020.01250.0457-0.07910.0435-0.04790.01440.0133-0.0520.15630.0123-0.00560.12030.01670.1317-18.3026-11.6066-101.1151
371.2693-0.18950.53060.9180.13672.4970.0840.10410.1306-0.1976-0.0216-0.2735-0.14310.4013-0.04140.1308-0.01070.06380.2244-0.01180.26239.858-13.0169-100.4205
382.3188-0.52610.44890.42960.01290.1645-0.0023-0.06430.0598-0.05370.0025-0.0528-0.01720.0136-0.00130.121-0.0125-0.00350.1131-0.00740.1175-11.7529-15.3578-87.0256
390.7151-0.4445-0.14512.05970.04180.17330.0421-0.04710.050.08850.024-0.17180.00620.0686-0.06660.09830.0027-0.03280.1106-0.0270.102-20.75197.2948-63.5782
400.1258-0.1064-0.02350.39880.09280.16390.0150.04310.0510.00310.0199-0.07770.00530.0122-0.04290.0954-0.0016-0.00990.1086-0.00010.1528-26.65350.1804-76.0327
411.08680.00310.34811.23890.58242.92380.07760.07560.1167-0.1509-0.03220.0459-0.2559-0.011-0.02530.11570.02460.01060.09440.02870.1635-49.325515.9489-81.0881
421.6942-1.0834-0.16280.95620.15040.29970.00990.04290.04640.01150.00050.01890.00640.017-0.01050.1272-0.0071-0.01990.10030.01170.0964-37.1677-5.8866-86.7206
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 67 )A6 - 67
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 316 )A68 - 316
3X-RAY DIFFRACTION3chain 'A' and (resid 317 through 391 )A317 - 391
4X-RAY DIFFRACTION4chain 'A' and (resid 392 through 483 )A392 - 483
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 102 )B6 - 102
6X-RAY DIFFRACTION6chain 'B' and (resid 103 through 292 )B103 - 292
7X-RAY DIFFRACTION7chain 'B' and (resid 293 through 400 )B293 - 400
8X-RAY DIFFRACTION8chain 'B' and (resid 401 through 483 )B401 - 483
9X-RAY DIFFRACTION9chain 'C' and (resid 8 through 102 )C8 - 102
10X-RAY DIFFRACTION10chain 'C' and (resid 103 through 235 )C103 - 235
11X-RAY DIFFRACTION11chain 'C' and (resid 236 through 292 )C236 - 292
12X-RAY DIFFRACTION12chain 'C' and (resid 293 through 400 )C293 - 400
13X-RAY DIFFRACTION13chain 'C' and (resid 401 through 441 )C401 - 441
14X-RAY DIFFRACTION14chain 'C' and (resid 442 through 483 )C442 - 483
15X-RAY DIFFRACTION15chain 'D' and (resid 7 through 102 )D7 - 102
16X-RAY DIFFRACTION16chain 'D' and (resid 103 through 292 )D103 - 292
17X-RAY DIFFRACTION17chain 'D' and (resid 293 through 400 )D293 - 400
18X-RAY DIFFRACTION18chain 'D' and (resid 401 through 483 )D401 - 483
19X-RAY DIFFRACTION19chain 'E' and (resid 8 through 102 )E8 - 102
20X-RAY DIFFRACTION20chain 'E' and (resid 103 through 235 )E103 - 235
21X-RAY DIFFRACTION21chain 'E' and (resid 236 through 270 )E236 - 270
22X-RAY DIFFRACTION22chain 'E' and (resid 271 through 292 )E271 - 292
23X-RAY DIFFRACTION23chain 'E' and (resid 293 through 316 )E293 - 316
24X-RAY DIFFRACTION24chain 'E' and (resid 317 through 350 )E317 - 350
25X-RAY DIFFRACTION25chain 'E' and (resid 351 through 400 )E351 - 400
26X-RAY DIFFRACTION26chain 'E' and (resid 401 through 441 )E401 - 441
27X-RAY DIFFRACTION27chain 'E' and (resid 442 through 483 )E442 - 483
28X-RAY DIFFRACTION28chain 'F' and (resid 8 through 102 )F8 - 102
29X-RAY DIFFRACTION29chain 'F' and (resid 103 through 235 )F103 - 235
30X-RAY DIFFRACTION30chain 'F' and (resid 236 through 270 )F236 - 270
31X-RAY DIFFRACTION31chain 'F' and (resid 271 through 350 )F271 - 350
32X-RAY DIFFRACTION32chain 'F' and (resid 351 through 391 )F351 - 391
33X-RAY DIFFRACTION33chain 'F' and (resid 392 through 441 )F392 - 441
34X-RAY DIFFRACTION34chain 'F' and (resid 442 through 483 )F442 - 483
35X-RAY DIFFRACTION35chain 'G' and (resid 7 through 102 )G7 - 102
36X-RAY DIFFRACTION36chain 'G' and (resid 103 through 292 )G103 - 292
37X-RAY DIFFRACTION37chain 'G' and (resid 293 through 400 )G293 - 400
38X-RAY DIFFRACTION38chain 'G' and (resid 401 through 483 )G401 - 483
39X-RAY DIFFRACTION39chain 'H' and (resid 7 through 102 )H7 - 102
40X-RAY DIFFRACTION40chain 'H' and (resid 103 through 292 )H103 - 292
41X-RAY DIFFRACTION41chain 'H' and (resid 293 through 400 )H293 - 400
42X-RAY DIFFRACTION42chain 'H' and (resid 401 through 483 )H401 - 483

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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