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- PDB-6ay1: Crystal structure of a nucleoside diphosphate kinase NDK from Hel... -

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基本情報

登録情報
データベース: PDB / ID: 6ay1
タイトルCrystal structure of a nucleoside diphosphate kinase NDK from Helicobacter pylori
要素Nucleoside diphosphate kinase
キーワードTRANSFERASE / NIAID / structural genomics / NDK / NDPK / kinase / ATP-dependent / Seattle Structural Genomics Center for Infectious Disease / SSGCID
機能・相同性
機能・相同性情報


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding / metal ion binding / cytoplasm
類似検索 - 分子機能
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits ...Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
HEXANE-1,6-DIOL / ISOPROPYL ALCOHOL / Nucleoside diphosphate kinase
類似検索 - 構成要素
生物種Helicobacter pylori (ピロリ菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.05 Å
データ登録者Edwards, T.E. / 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 a nucleoside diphosphate kinase NDK from Helicobacter pylori
著者: Edwards, T.E. / Dranow, D.M. / Lorimer, D.D.
履歴
登録2017年9月7日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年9月20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: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)131,44014
ポリマ－130,8478
非ポリマー5936
水5,891327
1
A: Nucleoside diphosphate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)16,4162
ポリマ－16,3561
非ポリマー601
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Nucleoside diphosphate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)16,5343
ポリマ－16,3561
非ポリマー1782
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Nucleoside diphosphate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)16,4742
ポリマ－16,3561
非ポリマー1181
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Nucleoside diphosphate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)16,4742
ポリマ－16,3561
非ポリマー1181
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: Nucleoside diphosphate kinase


分子量 (理論値)分子数
合計 (水以外)16,3561
ポリマ－16,3561
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: Nucleoside diphosphate kinase


分子量 (理論値)分子数
合計 (水以外)16,3561
ポリマ－16,3561
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
7
G: Nucleoside diphosphate kinase


分子量 (理論値)分子数
合計 (水以外)16,3561
ポリマ－16,3561
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
8
H: Nucleoside diphosphate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)16,4742
ポリマ－16,3561
非ポリマー1181
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)63.190, 93.400, 208.490
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 2 and (name N or name...
21(chain B and (resid 2 through 9 or (resid 10...
31(chain C and ((resid 2 and (name N or name...
41(chain D and (resid 2 through 9 or (resid 10...
51(chain E and (resid 2 through 9 or (resid 10...
61(chain G and (resid 2 through 11 or resid 13...
71(chain H and (resid 2 through 9 or (resid 10...

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
11LYSLYSLYSLYS(chain A and ((resid 2 and (name N or name...AA210
12HISHISLEULEU(chain A and ((resid 2 and (name N or name...AA0 - 1378 - 145
13HISHISLEULEU(chain A and ((resid 2 and (name N or name...AA0 - 1378 - 145
14HISHISLEULEU(chain A and ((resid 2 and (name N or name...AA0 - 1378 - 145
15HISHISLEULEU(chain A and ((resid 2 and (name N or name...AA0 - 1378 - 145
21LYSLYSILEILE(chain B and (resid 2 through 9 or (resid 10...BB2 - 910 - 17
22LYSLYSLYSLYS(chain B and (resid 2 through 9 or (resid 10...BB1018
23METMETLEULEU(chain B and (resid 2 through 9 or (resid 10...BB1 - 1379 - 145
24METMETLEULEU(chain B and (resid 2 through 9 or (resid 10...BB1 - 1379 - 145
25METMETLEULEU(chain B and (resid 2 through 9 or (resid 10...BB1 - 1379 - 145
26METMETLEULEU(chain B and (resid 2 through 9 or (resid 10...BB1 - 1379 - 145
31LYSLYSLYSLYS(chain C and ((resid 2 and (name N or name...CC210
32METMETLEULEU(chain C and ((resid 2 and (name N or name...CC1 - 1379 - 145
33METMETLEULEU(chain C and ((resid 2 and (name N or name...CC1 - 1379 - 145
34METMETLEULEU(chain C and ((resid 2 and (name N or name...CC1 - 1379 - 145
35METMETLEULEU(chain C and ((resid 2 and (name N or name...CC1 - 1379 - 145
41LYSLYSILEILE(chain D and (resid 2 through 9 or (resid 10...DD2 - 910 - 17
42LYSLYSLYSLYS(chain D and (resid 2 through 9 or (resid 10...DD1018
43METMETLEULEU(chain D and (resid 2 through 9 or (resid 10...DD1 - 1379 - 145
44METMETLEULEU(chain D and (resid 2 through 9 or (resid 10...DD1 - 1379 - 145
45METMETLEULEU(chain D and (resid 2 through 9 or (resid 10...DD1 - 1379 - 145
46METMETLEULEU(chain D and (resid 2 through 9 or (resid 10...DD1 - 1379 - 145
51LYSLYSILEILE(chain E and (resid 2 through 9 or (resid 10...EE2 - 910 - 17
52LYSLYSLYSLYS(chain E and (resid 2 through 9 or (resid 10...EE1018
53LYSLYSLEULEU(chain E and (resid 2 through 9 or (resid 10...EE2 - 13710 - 145
54LYSLYSLEULEU(chain E and (resid 2 through 9 or (resid 10...EE2 - 13710 - 145
55LYSLYSLEULEU(chain E and (resid 2 through 9 or (resid 10...EE2 - 13710 - 145
56LYSLYSLEULEU(chain E and (resid 2 through 9 or (resid 10...EE2 - 13710 - 145
61LYSLYSPROPRO(chain G and (resid 2 through 11 or resid 13...GG2 - 1110 - 19
62ALAALALYSLYS(chain G and (resid 2 through 11 or resid 13...GG13 - 1621 - 24
63LYSLYSLYSLYS(chain G and (resid 2 through 11 or resid 13...GG1725
64LYSLYSLEULEU(chain G and (resid 2 through 11 or resid 13...GG2 - 13710 - 145
65LYSLYSLEULEU(chain G and (resid 2 through 11 or resid 13...GG2 - 13710 - 145
66LYSLYSLEULEU(chain G and (resid 2 through 11 or resid 13...GG2 - 13710 - 145
67LYSLYSLEULEU(chain G and (resid 2 through 11 or resid 13...GG2 - 13710 - 145
71LYSLYSILEILE(chain H and (resid 2 through 9 or (resid 10...HH2 - 910 - 17
72LYSLYSLYSLYS(chain H and (resid 2 through 9 or (resid 10...HH1018
73METMETLEULEU(chain H and (resid 2 through 9 or (resid 10...HH1 - 1379 - 145
74METMETLEULEU(chain H and (resid 2 through 9 or (resid 10...HH1 - 1379 - 145
75METMETLEULEU(chain H and (resid 2 through 9 or (resid 10...HH1 - 1379 - 145
76METMETLEULEU(chain H and (resid 2 through 9 or (resid 10...HH1 - 1379 - 145

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要素

#1: タンパク質
Nucleoside diphosphate kinase / NDK / NDP kinase / Nucleoside-2-P kinase


分子量: 16355.909 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Helicobacter pylori (ピロリ菌) / 遺伝子: ndk, HPG27_182 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: B5Z9W9, nucleoside-diphosphate kinase
#2: 化合物 ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / 2-プロパノ-ル


分子量: 60.095 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O / コメント: alkaloid*YM
#3: 化合物 ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / (S)-2-メチル-2,4-ペンタンジオ-ル


分子量: 118.174 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C6H14O2 / コメント: 沈殿剤*YM
#4: 化合物 ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-ヘキサンジオ-ル


分子量: 118.174 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C6H14O2
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 327 / 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: 2.43 Å3/Da / 溶媒含有率: 49.41 %
結晶化温度: 289 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5
詳細: 24 mg/mL HepyC.00923.a.B1.PW38239 in 6 mM AMPPNP + magnesium chloride against Morpheus screen condition D12 with 12.5% PEG1000, 12.5% PEG 3350, 12.5% MPD, 20 mM alcohols (1,6-hexanediol, 1- ...詳細: 24 mg/mL HepyC.00923.a.B1.PW38239 in 6 mM AMPPNP + magnesium chloride against Morpheus screen condition D12 with 12.5% PEG1000, 12.5% PEG 3350, 12.5% MPD, 20 mM alcohols (1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol), 0.1 M bicine/Trizma base, pH 8.5, crystal tracking ID 291403d12, unique puck ID rmz3-8

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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: 0.97982 Å
検出器タイプ: RAYONIX MX-300 / 検出器: CCD / 日付: 2017年8月18日
放射モノクロメーター: diamond(111) / 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: 0.97982 Å / 相対比: 1
反射解像度: 2.05→45.571 Å / Num. obs: 78186 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / 冗長度: 5.926 % / Biso Wilson estimate: 35.51 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.072 / Χ2: 1.036 / Net I/σ(I): 14.61
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
2.05-2.16.1690.5173.2557030.9380.565100
2.1-2.166.1670.4094.155450.9550.44799.9
2.16-2.226.10.3125.2854410.9750.34299.9
2.22-2.296.0950.2666.2252600.9760.29199.9
2.29-2.376.080.237.0151090.9830.25299.9
2.37-2.456.0210.1798.5649770.9890.19799.9
2.45-2.545.9970.169.647720.9890.175100
2.54-2.655.9370.1311.545900.9910.14399.9
2.65-2.765.9170.1113.4744290.9930.12299.8
2.76-2.95.8750.0916.2542460.9940.09999.7
2.9-3.065.7780.07718.8340210.9950.08599.8
3.06-3.245.760.06821.6538050.9950.07499.6
3.24-3.475.6970.0624.5536210.9960.06799.7
3.47-3.745.6530.05526.6833900.9960.06199.9
3.74-4.15.6590.05228.3230850.9960.05799.6
4.1-4.585.6640.04729.9228310.9970.05299.6
4.58-5.295.7690.04330.3325250.9980.047100
5.29-6.485.9140.0430.4121440.9980.044100
6.48-9.175.7680.03630.9817140.9990.039100
9.17-45.5715.1620.03830.159780.9970.04297.5

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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
XSCALEデータスケーリング
MOLREP位相決定
PHENIX精密化
PDB_EXTRACT3.22データ抽出
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 4HR2

4hr2


解像度: 2.05→45.571 Å / SU ML: 0.28 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 29.12
Rfactor反射数%反射
Rfree0.2408 1994 2.55 %
Rwork0.2064 --
obs0.2073 78092 99.72 %
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: 152.84 Å2 / Biso mean: 62.9576 Å2 / Biso min: 19.77 Å2
精密化ステップサイクル: final / 解像度: 2.05→45.571 Å
タンパク質核酸リガンド溶媒全体
原子数7746 0 40 327 8113
Biso mean--70.85 49.09 -
残基数----1055
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0077928
X-RAY DIFFRACTIONf_angle_d0.82310723
X-RAY DIFFRACTIONf_chiral_restr0.0551250
X-RAY DIFFRACTIONf_plane_restr0.0061411
X-RAY DIFFRACTIONf_dihedral_angle_d13.0554801
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A3484X-RAY DIFFRACTION8.869TORSIONAL
12B3484X-RAY DIFFRACTION8.869TORSIONAL
13C3484X-RAY DIFFRACTION8.869TORSIONAL
14D3484X-RAY DIFFRACTION8.869TORSIONAL
15E3484X-RAY DIFFRACTION8.869TORSIONAL
16G3484X-RAY DIFFRACTION8.869TORSIONAL
17H3484X-RAY DIFFRACTION8.869TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0499-2.10120.2881350.274953335468
2.1012-2.1580.31161390.259153665505
2.158-2.22150.29921400.245953445484
2.2215-2.29320.25421300.235853985528
2.2932-2.37520.29011050.237354075512
2.3752-2.47030.291480.233853875535
2.4703-2.58270.27571470.240853845531
2.5827-2.71880.28911500.235554105560
2.7188-2.88920.28411740.233654055579
2.8892-3.11220.27331180.222554385556
3.1122-3.42530.25621390.204954515590
3.4253-3.92070.21511820.193654615643
3.9207-4.93870.19971490.161555415690
4.9387-45.5820.20491380.194457735911
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)
14.65673.1743-1.81759.2663-2.11592.63590.00370.14210.3451-0.13310.14050.6311-0.43470.2111-0.1120.56110.0240.02070.24690.00790.3289-4.9011-6.1909-79.1052
24.738-0.67892.16385.65972.63932.56670.13240.38090.07250.001-0.1208-0.15550.11710.2610.08460.1402-0.02430.07960.27940.0010.3212-0.1192-10.1-48.6925
33.10051.80730.61027.81611.07493.02150.10320.18460.1759-0.0302-0.02210.1552-0.0659-0.1408-0.10920.19580.03340.0310.2128-0.02340.2035-3.1174-8.6584-47.5422
46.0445-2.97782.62522.63540.07962.73860.4491.5333-2.26-0.4332-0.15330.42431.27350.6062-0.4460.58540.0351-0.06790.5956-0.2590.7722-9.5354-26.6657-54.1338
53.7641-0.3986-0.47512.5992-0.37056.0955-0.03590.0336-0.76510.4413-0.2446-0.27840.325-0.07980.23990.14580.00660.00830.2112-0.04660.3055-5.4888-15.8021-46.9614
64.2731-4.4444.49767.9007-5.22674.82340.40420.8972-0.3278-1.1944-0.3605-1.02570.3910.8375-0.04380.38240.02270.14350.4021-0.07610.46124.9207-10.9189-58.5806
77.7871-1.8759-1.60423.77095.73388.9464-0.22990.1497-0.6840.28150.5992-1.0730.82610.7286-0.37320.36360.04070.01730.3331-0.05340.57079.9512-19.0945-50.157
84.6852-5.0130.60247.58970.63843.12250.24310.1324-0.3057-0.3287-0.20760.20690.0684-0.104-0.04890.2114-0.07730.03240.25030.01620.3343-6.3819-12.0611-54.0669
99.2747-0.85870.02566.288-1.11146.6928-0.2875-0.7699-0.22740.37940.41030.24880.365-0.3521-0.20770.23350.00560.05140.26840.00210.2924-3.07931.3994-29.8889
102.4899-2.16011.75733.9813-1.98436.38120.0104-0.02420.0263-0.12550.0005-0.20320.06220.2778-0.02630.2081-0.03240.0560.221-0.01710.39352.46491.6756-40.4603
113.7836-2.04173.60612.1385-1.68793.50590.1933-0.30160.2146-0.16150.11270.9344-0.2292-0.6301-0.28310.32190.02540.00090.35550.01710.4625-12.897413.7521-40.5853
125.5207-1.0376-1.97499.25793.04239.32680.1247-0.29120.93140.0810.10540.2021-0.9408-0.11-0.15220.27380.01020.01930.2132-0.0320.4183-6.700220.2011-38.2823
136.9038-5.60945.31294.5695-4.31294.0866-0.2428-0.4988-0.09780.30640.0262-0.0202-0.1204-0.39570.06620.2813-0.03040.02370.2888-0.01670.3899-2.03040.177-32.6698
149.02260.6204-7.27712.9705-3.75769.55790.0166-0.40950.0240.48780.2407-1.00170.14390.2091-0.10720.334-0.0059-0.08020.2519-0.07670.40314.80715.3601-27.6116
157.9130.80791.5148.29925.4749.3368-0.30970.10870.4121-0.00460.2908-1.0681-0.05880.5924-0.02230.2013-0.00990.04530.2968-0.0360.520211.093412.5912-34.4327
165.63894.9762-5.31464.3937-4.6814.9646-0.1136-0.31640.6482-0.03240.2287-0.2498-0.35940.3228-0.22380.3404-0.03170.03330.4011-0.06040.52012.711713.6793-35.6495
177.56745.0212.6785.29420.34172.08210.034-0.33740.09060.306-0.19650.5538-0.0646-0.26570.13150.2540.05130.12790.3201-0.00070.4457-11.66052.5844-30.6519
184.08594.23761.21817.13553.42832.09450.1027-0.27150.7391-0.0493-0.72861.0476-0.483-0.66020.50320.37080.01580.03480.4055-0.04390.6728-30.80113.6199-30.4327
197.7083-1.71425.50425.4864-2.01434.086-0.23110.3296-1.0816-0.0740.41970.78311.0865-1.0725-0.19310.4089-0.12890.11820.5479-0.04160.6079-37.0772-12.006-40.2208
200.3524-1.6122-0.54217.67981.31434.3356-0.04630.10770.4196-0.07550.00070.2483-0.1153-0.35270.02340.2155-0.02240.02940.45070.05250.5116-35.73581.3188-38.4169
212.9088-2.8837-2.43912.87382.05978.2386-0.1607-0.182-0.66920.22730.1513-0.748210.74640.06950.42740.08340.04890.44920.06960.5865-20.8644-13.2494-32.2886
228.23415.4623-3.78074.2589-3.61767.38680.2376-2.1313-1.20732.0083-0.09860.49431.32940.0237-0.08981.19780.04820.28330.81050.19290.6297-25.9839-16.3167-20.9879
233.3234-1.43993.87667.496-3.27514.88640.0973-0.6664-0.92850.38670.5511.28571.271-0.3029-0.58940.6203-0.00380.19710.5130.08750.8177-28.2841-18.2365-32.0915
244.80221.27931.73028.0441.12392.5038-0.145-0.67230.79030.56480.09840.7505-0.2328-0.2445-0.00220.27320.04890.07120.5797-0.02420.5395-35.09362.0542-29.6861
255.6719-0.74020.50427.3538-4.48387.5185-0.30840.2053-0.62130.6470.90371.05810.2218-0.8352-0.45860.36620.03270.06890.8080.20330.5594-45.73-9.5959-25.7438
267.3292-6.07185.18365.035-4.29153.6725-0.1533-0.5001-1.005-0.31020.26480.72460.9335-0.4987-0.21310.4327-0.07630.10210.56450.04050.589-41.6484-11.596-31.4288
273.69240.15820.89746.44292.59632.014-0.2012-0.49910.18420.5204-0.0148-0.01780.1052-0.04790.22030.25310.00270.0510.59320.04580.4393-26.1248-1.602-26.6071
286.38165.9839-4.01066.0351-4.72034.6879-0.39270.60310.4354-0.4433-0.13540.701-0.3903-0.77330.57330.3081-0.0066-0.04430.3931-0.00490.5551-19.5875.088-36.719
299.1074-2.8757-2.87243.48911.60877.7730.32280.79510.5659-0.0573-0.30350.1904-0.3068-0.9124-0.02970.22520.03220.05880.46440.06780.5073-33.32873.2818-51.6332
301.4957-0.07722.91119.20282.98347.1580.29790.53130.0223-0.2211-0.40681.08150.2231-0.93960.08360.3026-0.00710.00090.73020.02160.6928-41.1472-1.2499-48.7744
315.59983.4197-1.01118.5622-0.38313.0103-0.01810.66320.1527-0.6770.09090.2868-0.1022-0.2069-0.09480.24130.1038-0.01250.4880.02120.3952-28.16015.4848-55.8941
325.9814-4.46211.34693.97370.65066.55470.51820.29881.0188-0.6371-0.28710.7082-1.359-1.7554-0.45030.71660.19670.03070.83260.19410.8478-44.037710.0353-60.7277
338.24660.643-3.85177.8768-1.63276.95660.38150.570.3452-0.08230.13021.4514-1.1993-0.9781-0.62440.53450.2138-0.05380.78010.16240.6622-40.221111.5591-55.1629
346.843-5.28254.48828.7204-3.24795.95650.08180.1946-0.5277-0.69140.0690.41480.1529-0.2795-0.11850.25610.02140.04620.4609-0.00650.4043-24.7754-3.1378-58.2329
354.12420.3384-2.27065.1651-2.56623.37270.2709-0.0450.5805-1.68530.3281-0.4971-0.38420.3317-0.54021.1922-0.19160.2580.4428-0.14950.65552.304913.1902-86.7884
368.8665-4.245-5.99415.98115.26927.8523-0.1083-2.751.65871.50951.5339-0.5588-1.03261.2716-1.17141.04740.13190.15610.9606-0.26660.6168-7.881417.8-71.0408
370.46061.09570.19362.67790.64421.404-0.0522-0.08361.0326-0.71270.5314-0.6641-1.15460.475-0.36211.0616-0.20490.20560.5252-0.2090.90032.650217.913-81.3878
380.5196-0.63560.52793.6126-0.64931.7492-0.07450.00220.806-0.0922-0.0674-0.2915-0.6509-0.02990.08971.5596-0.22450.33870.3818-0.13781.20723.456926.4647-83.5423
392.89711.43820.74434.0357-0.55912.5455-0.2389-0.91460.1563-0.92090.5227-0.631-0.40240.2175-0.13590.6447-0.07340.11980.4793-0.04050.49082.15875.5214-79.5429
401.17310.26910.28280.596-1.22343.13620.18130.21580.3504-1.21070.2551-0.3927-0.0615-0.031-0.03882.0746-0.09910.57080.56510.07710.84576.168811.9723-100.4212
413.44251.7271.71921.15960.13934.17620.11070.9145-0.1768-0.25730.1879-0.13560.03550.159-0.07912.40470.13510.06980.8221-0.03930.52024.2688-5.9717-110.4793
426.03542.44.1944.8651-3.61451.99980.12990.191-1.03890.64160.2469-0.44652.20770.8986-0.28022.22890.2350.16860.61970.00930.784211.4043-5.4031-108.3661
430.6253-0.87920.94381.2826-1.3381.41510.14130.5150.2365-1.1589-0.01770.0641-0.28360.0099-0.01822.686-0.20320.10160.45030.27630.4388-0.37598.1531-106.4883
440.8014-0.56720.28471.4633-1.1991.022-0.0707-0.047-0.2034-0.69020.21140.77260.128-0.2256-0.33511.43790.2665-0.7050.49270.03951.0119-23.8738-6.1018-94.4382
451.7575-1.117-0.34182.6377-0.13912.2627-0.02860.12-0.5845-1.3204-0.22631.0132-0.1148-0.18350.17921.31860.1912-0.65480.4431-0.01231.0256-20.9885-12.4015-95.2725
460.59190.5993-0.96430.928-0.61632.01990.25120.33750.4684-0.05660.32160.8024-0.5619-0.6096-0.47521.65490.3353-0.80970.57850.24131.3218-26.33979.8266-94.9984
470.9661-0.02220.43070.464-0.99472.26940.28980.1453-0.3136-0.31910.210.3020.1804-0.3995-0.12811.4590.157-0.75270.5079-0.00351.0073-20.3501-4.0505-94.9867
482.6012-0.3463.03120.4104-0.9064.22250.0352-0.3297-0.2122-0.04190.15890.05950.1357-0.1866-0.10431.38750.2461-0.99450.7920.00291.1141-27.7498-11.0811-105.5888
496.95340.21040.40310.1227-1.01659.1205-0.1724-0.15020.245-0.09130.60660.4489-0.5283-1.6987-0.36280.98880.1876-0.8031.04290.1231.8176-35.0037-8.6733-94.7385
501.9866-0.69941.38761.0592-1.60762.64480.0054-0.3036-0.1538-0.24290.22090.5377-0.215-0.6425-0.68611.70780.2826-0.80460.76990.17410.8771-25.5449-0.3765-100.8131
511.52880.5706-0.4920.9798-0.97150.9655-0.1558-0.2508-0.0825-0.1181-0.1954-0.12510.25440.58660.25891.9347-0.1314-0.35830.64490.15820.5228-7.984-3.1605-101.838
524.28280.45080.68116.3542-0.08736.11310.09870.07960.1811-0.2891-0.01360.5042-0.5044-0.4985-0.080.31640.0103-0.09570.25990.07330.3884-11.5317-11.5366-77.9387
532.8248-0.15041.12920.5171.23224.0150.32240.4873-0.3214-1.0392-0.17930.59830.3648-0.2255-0.13261.0856-0.0257-0.30110.4474-0.01110.5821-11.6808-21.4735-94.0637
540.47460.90680.64344.0277-1.38463.89210.06970.05680.1572-0.77210.08831.5404-0.1505-0.3139-0.20770.57120.0914-0.2550.38290.04490.6868-17.9132-13.5073-85.1034
554.90682.07932.07036.41934.38527.02340.12140.1286-0.1976-1.1550.1211-0.30560.86641.1611-0.33980.62260.10530.02520.455-0.00790.28744.5391-17.6522-86.5195
563.4464-4.82874.88098.0578-5.21549.03570.37790.5934-0.4288-2.141-0.0320.27960.68390.8422-0.27950.9234-0.00560.03050.3735-0.00960.40161.1048-21.2741-92.3853
575.9024-3.39781.56716.03162.74373.683-0.0862-0.2921-0.3217-0.41210.29921.3793-0.5129-0.2013-0.18180.39560.0275-0.08930.2880.11590.5809-13.6781-15.6567-77.6445
585.01511.25340.60335.9032-5.8897.2274-0.23260.0562-0.2217-0.85990.21090.87850.118-0.3408-0.10830.4472-0.0201-0.16860.31380.03670.7674-13.2594-29.4342-82.2263
595.5397-2.2555-1.0766.2323-0.56981.96320.06070.4386-0.4993-0.7132-0.13560.3013-0.00010.08890.14850.4742-0.0155-0.07220.28090.04370.372-6.6549-23.8323-83.6216
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 121 through 137 )H121 - 137
2X-RAY DIFFRACTION2chain 'A' and (resid 0 through 18 )A0 - 18
3X-RAY DIFFRACTION3chain 'A' and (resid 19 through 49 )A19 - 49
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 58 )A50 - 58
5X-RAY DIFFRACTION5chain 'A' and (resid 59 through 79 )A59 - 79
6X-RAY DIFFRACTION6chain 'A' and (resid 80 through 89 )A80 - 89
7X-RAY DIFFRACTION7chain 'A' and (resid 90 through 106 )A90 - 106
8X-RAY DIFFRACTION8chain 'A' and (resid 107 through 137 )A107 - 137
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 9 )B1 - 9
10X-RAY DIFFRACTION10chain 'B' and (resid 10 through 39 )B10 - 39
11X-RAY DIFFRACTION11chain 'B' and (resid 40 through 49 )B40 - 49
12X-RAY DIFFRACTION12chain 'B' and (resid 50 through 70 )B50 - 70
13X-RAY DIFFRACTION13chain 'B' and (resid 71 through 80 )B71 - 80
14X-RAY DIFFRACTION14chain 'B' and (resid 81 through 89 )B81 - 89
15X-RAY DIFFRACTION15chain 'B' and (resid 90 through 106 )B90 - 106
16X-RAY DIFFRACTION16chain 'B' and (resid 107 through 120 )B107 - 120
17X-RAY DIFFRACTION17chain 'B' and (resid 121 through 137 )B121 - 137
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 9 )C1 - 9
19X-RAY DIFFRACTION19chain 'C' and (resid 10 through 18 )C10 - 18
20X-RAY DIFFRACTION20chain 'C' and (resid 19 through 39 )C19 - 39
21X-RAY DIFFRACTION21chain 'C' and (resid 40 through 49 )C40 - 49
22X-RAY DIFFRACTION22chain 'C' and (resid 50 through 58 )C50 - 58
23X-RAY DIFFRACTION23chain 'C' and (resid 59 through 70 )C59 - 70
24X-RAY DIFFRACTION24chain 'C' and (resid 71 through 89 )C71 - 89
25X-RAY DIFFRACTION25chain 'C' and (resid 90 through 101 )C90 - 101
26X-RAY DIFFRACTION26chain 'C' and (resid 102 through 114 )C102 - 114
27X-RAY DIFFRACTION27chain 'C' and (resid 115 through 131 )C115 - 131
28X-RAY DIFFRACTION28chain 'C' and (resid 132 through 137 )C132 - 137
29X-RAY DIFFRACTION29chain 'D' and (resid 1 through 18 )D1 - 18
30X-RAY DIFFRACTION30chain 'D' and (resid 19 through 29 )D19 - 29
31X-RAY DIFFRACTION31chain 'D' and (resid 30 through 89 )D30 - 89
32X-RAY DIFFRACTION32chain 'D' and (resid 90 through 101 )D90 - 101
33X-RAY DIFFRACTION33chain 'D' and (resid 102 through 114 )D102 - 114
34X-RAY DIFFRACTION34chain 'D' and (resid 115 through 137 )D115 - 137
35X-RAY DIFFRACTION35chain 'E' and (resid 2 through 49 )E2 - 49
36X-RAY DIFFRACTION36chain 'E' and (resid 50 through 58 )E50 - 58
37X-RAY DIFFRACTION37chain 'E' and (resid 59 through 101 )E59 - 101
38X-RAY DIFFRACTION38chain 'E' and (resid 102 through 114 )E102 - 114
39X-RAY DIFFRACTION39chain 'E' and (resid 115 through 137 )E115 - 137
40X-RAY DIFFRACTION40chain 'F' and (resid 4 through 40 )F4 - 40
41X-RAY DIFFRACTION41chain 'F' and (resid 41 through 58 )F41 - 58
42X-RAY DIFFRACTION42chain 'F' and (resid 59 through 67 )F59 - 67
43X-RAY DIFFRACTION43chain 'F' and (resid 68 through 137 )F68 - 137
44X-RAY DIFFRACTION44chain 'G' and (resid 2 through 18 )G2 - 18
45X-RAY DIFFRACTION45chain 'G' and (resid 19 through 39 )G19 - 39
46X-RAY DIFFRACTION46chain 'G' and (resid 40 through 66 )G40 - 66
47X-RAY DIFFRACTION47chain 'G' and (resid 67 through 78 )G67 - 78
48X-RAY DIFFRACTION48chain 'G' and (resid 79 through 88 )G79 - 88
49X-RAY DIFFRACTION49chain 'G' and (resid 89 through 106 )G89 - 106
50X-RAY DIFFRACTION50chain 'G' and (resid 107 through 131 )G107 - 131
51X-RAY DIFFRACTION51chain 'G' and (resid 132 through 137 )G132 - 137
52X-RAY DIFFRACTION52chain 'H' and (resid 1 through 9 )H1 - 9
53X-RAY DIFFRACTION53chain 'H' and (resid 10 through 18 )H10 - 18
54X-RAY DIFFRACTION54chain 'H' and (resid 19 through 39 )H19 - 39
55X-RAY DIFFRACTION55chain 'H' and (resid 40 through 58 )H40 - 58
56X-RAY DIFFRACTION56chain 'H' and (resid 59 through 70 )H59 - 70
57X-RAY DIFFRACTION57chain 'H' and (resid 71 through 89 )H71 - 89
58X-RAY DIFFRACTION58chain 'H' and (resid 90 through 106 )H90 - 106
59X-RAY DIFFRACTION59chain 'H' and (resid 107 through 120 )H107 - 120

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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://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