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- PDB-6aqz: Crystal structure of a gdp-l-fucose synthetase from Naegleria fow... -

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基本情報

登録情報
データベース: PDB / ID: 6aqz
タイトルCrystal structure of a gdp-l-fucose synthetase from Naegleria fowleri bound to NADP
要素gdp-l-fucose synthetase
キーワードOXIDOREDUCTASE (酸化還元酵素) / NIAID / structural genomics (構造ゲノミクス) / Seattle Structural Genomics Center for Infectious Disease / SSGCID
機能・相同性
機能・相同性情報


GDP-L-フコースシンターゼ / GDP-L-fucose synthase activity / 'de novo' GDP-L-fucose biosynthetic process
類似検索 - 分子機能
GDP-L-fucose synthase/GDP-L-colitose synthase / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / ロスマンフォールド / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / GDP-L-フコースシンターゼ
類似検索 - 構成要素
生物種Naegleria fowleri (フォーラーネグレリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.4 Å
データ登録者Seattle Structural Genomics Center for Infectious Disease / 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 gdp-l-fucose synthetase from Naegleria fowleri bound to NADP
著者: Edwards, T.E. / Dranow, D.M. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease
履歴
登録2017年8月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年8月30日Provider: repository / タイプ: Initial release
改定 1.12017年10月18日Group: Data collection
カテゴリ: diffrn_detector / diffrn_radiation_wavelength / diffrn_source
Item: _diffrn_detector.type / _diffrn_radiation_wavelength.wavelength
改定 1.22018年3月7日Group: Data collection / カテゴリ: diffrn_source / Item: _diffrn_source.source
改定 1.32023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: gdp-l-fucose synthetase
B: gdp-l-fucose synthetase
C: gdp-l-fucose synthetase
D: gdp-l-fucose synthetase
E: gdp-l-fucose synthetase
F: gdp-l-fucose synthetase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)237,93812
ポリマ－234,1586
非ポリマー3,7796
水4,504250
1
A: gdp-l-fucose synthetase
B: gdp-l-fucose synthetase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)79,6025
ポリマ－78,0532
非ポリマー1,5493
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-28 kcal/mol
Surface area28030 Å2
手法PISA
2
C: gdp-l-fucose synthetase
D: gdp-l-fucose synthetase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)78,7963
ポリマ－78,0532
非ポリマー7431
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-26 kcal/mol
Surface area28460 Å2
手法PISA
3
E: gdp-l-fucose synthetase
F: gdp-l-fucose synthetase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)79,5404
ポリマ－78,0532
非ポリマー1,4872
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-30 kcal/mol
Surface area26550 Å2
手法PISA
単位格子
Length a, b, c (Å)97.370, 104.030, 120.170
Angle α, β, γ (deg.)90.000, 108.670, 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 5 through 6 and (name N...
21(chain B and ((resid 5 through 6 and (name N...
31(chain C and ((resid 5 through 6 and (name N...
41(chain D and ((resid 5 through 6 and (name N...
51(chain E and (resid 5 through 40 or resid 42...
61(chain F and ((resid 5 through 6 and (name N...

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
11GLUGLUVALVAL(chain A and ((resid 5 through 6 and (name N...AA5 - 613 - 14
12HISHISNAPNAP(chain A and ((resid 5 through 6 and (name N...AA - G0 - 4018
13HISHISNAPNAP(chain A and ((resid 5 through 6 and (name N...AA - G0 - 4018
14HISHISNAPNAP(chain A and ((resid 5 through 6 and (name N...AA - G0 - 4018
15HISHISNAPNAP(chain A and ((resid 5 through 6 and (name N...AA - G0 - 4018
21GLUGLUVALVAL(chain B and ((resid 5 through 6 and (name N...BB5 - 613 - 14
22ARGARGNAPNAP(chain B and ((resid 5 through 6 and (name N...BB - H4 - 40112
23ARGARGNAPNAP(chain B and ((resid 5 through 6 and (name N...BB - H4 - 40112
24ARGARGNAPNAP(chain B and ((resid 5 through 6 and (name N...BB - H4 - 40112
25ARGARGNAPNAP(chain B and ((resid 5 through 6 and (name N...BB - H4 - 40112
31GLUGLUVALVAL(chain C and ((resid 5 through 6 and (name N...CC5 - 613 - 14
32HISHISNAPNAP(chain C and ((resid 5 through 6 and (name N...CC - J0 - 4018
33HISHISNAPNAP(chain C and ((resid 5 through 6 and (name N...CC - J0 - 4018
34HISHISNAPNAP(chain C and ((resid 5 through 6 and (name N...CC - J0 - 4018
35HISHISNAPNAP(chain C and ((resid 5 through 6 and (name N...CC - J0 - 4018
41GLUGLUVALVAL(chain D and ((resid 5 through 6 and (name N...DD5 - 613 - 14
42METMETLYSLYS(chain D and ((resid 5 through 6 and (name N...DD1 - 3339 - 341
43METMETLYSLYS(chain D and ((resid 5 through 6 and (name N...DD1 - 3339 - 341
44METMETLYSLYS(chain D and ((resid 5 through 6 and (name N...DD1 - 3339 - 341
45METMETLYSLYS(chain D and ((resid 5 through 6 and (name N...DD1 - 3339 - 341
51GLUGLUGLNGLN(chain E and (resid 5 through 40 or resid 42...EE5 - 4013 - 48
52LYSLYSLYSLYS(chain E and (resid 5 through 40 or resid 42...EE42 - 6250 - 70
53GLNGLNGLNGLN(chain E and (resid 5 through 40 or resid 42...EE6371
54GLUGLUNAPNAP(chain E and (resid 5 through 40 or resid 42...EE - K5 - 40113
55GLUGLUNAPNAP(chain E and (resid 5 through 40 or resid 42...EE - K5 - 40113
56GLUGLUNAPNAP(chain E and (resid 5 through 40 or resid 42...EE - K5 - 40113
57GLUGLUNAPNAP(chain E and (resid 5 through 40 or resid 42...EE - K5 - 40113
61GLUGLUVALVAL(chain F and ((resid 5 through 6 and (name N...FF5 - 613 - 14
62GLUGLUNAPNAP(chain F and ((resid 5 through 6 and (name N...FF - L5 - 40113
63GLUGLUNAPNAP(chain F and ((resid 5 through 6 and (name N...FF - L5 - 40113
64GLUGLUNAPNAP(chain F and ((resid 5 through 6 and (name N...FF - L5 - 40113
65GLUGLUNAPNAP(chain F and ((resid 5 through 6 and (name N...FF - L5 - 40113

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要素

#1: タンパク質
gdp-l-fucose synthetase


分子量: 39026.402 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Naegleria fowleri (フォーラーネグレリア)
株: ATCC 30863 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A2D0TCK0*PLUS
#2: 化合物
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / ニコチンアミドアデニンジヌクレオチドリン酸


分子量: 743.405 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C21H28N7O17P3
#3: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル / エチレングリコール


分子量: 62.068 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C2H6O2
#4: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 250 / 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: 2.46 Å3/Da / 溶媒含有率: 50.05 %
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: 7.5
詳細: NafoA.00085.a.B1.PS38274 at 12 mg/mL with 2 mM NADP against MCSG1 screen condition H11 0.2 M NaCl, 0.1 M HEPES pH 7.5, 25% PEG 3350 supplemented with 15% EG as cryo, crystal tracking ID ...詳細: NafoA.00085.a.B1.PS38274 at 12 mg/mL with 2 mM NADP against MCSG1 screen condition H11 0.2 M NaCl, 0.1 M HEPES pH 7.5, 25% PEG 3350 supplemented with 15% EG as cryo, crystal tracking ID 292643h11, unique puck ID dhq2-6

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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: 1 Å
検出器タイプ: RAYONIX MX300HE / 検出器: CCD / 日付: 2017年8月7日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 2.4→46.123 Å / Num. obs: 87872 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / 冗長度: 3.778 % / Biso Wilson estimate: 53.45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.059 / Χ2: 1.022 / Net I/σ(I): 14.96
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
2.4-2.463.8540.5792.1465130.8240.67398.8
2.46-2.533.8490.4412.7562750.8990.51399.1
2.53-2.63.8490.3733.3161820.9210.43398.9
2.6-2.683.850.2914.2259520.9470.33899
2.68-2.773.8470.2275.4557600.9670.26498.9
2.77-2.873.8390.1736.8456230.9820.20198.9
2.87-2.983.8320.1378.754220.9870.15999.2
2.98-3.13.8320.10111.4851840.9920.11898.8
3.1-3.243.8070.08114.1450030.9940.09498.7
3.24-3.393.790.06517.4247430.9960.07698.6
3.39-3.583.7620.05221.6145320.9970.0698.8
3.58-3.793.7260.04224.9842850.9980.04998.7
3.79-4.063.7020.03827.6240410.9980.04598.6
4.06-4.383.6820.03630.1537740.9970.04299
4.38-4.83.6650.03332.0634830.9980.03998.8
4.8-5.373.6510.03332.0531270.9980.03898.5
5.37-6.23.6410.03331.9727830.9980.03898.6
6.2-7.593.6110.0333.3223710.9980.03598.9
7.59-10.733.5730.02634.8618390.9990.0398.9
10.73-46.1233.3520.02934.159800.9970.03492.7

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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
PHENIX(1.12_2829: ???)精密化
PDB_EXTRACT3.22データ抽出
XDSデータ削減
MOLREP位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4e5y

4e5y


解像度: 2.4→46.123 Å / SU ML: 0.33 / 交差検証法: THROUGHOUT / σ(F): 1.36 / 位相誤差: 26.21
Rfactor反射数%反射
Rfree0.2244 2041 2.32 %
Rwork0.1778 --
obs0.1789 87834 98.82 %
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: 175.65 Å2 / Biso mean: 67.0213 Å2 / Biso min: 27.74 Å2
精密化ステップサイクル: final / 解像度: 2.4→46.123 Å
タンパク質核酸リガンド溶媒全体
原子数14847 0 244 250 15341
Biso mean--56.36 53.41 -
残基数----1949
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00815507
X-RAY DIFFRACTIONf_angle_d0.95321147
X-RAY DIFFRACTIONf_chiral_restr0.0542307
X-RAY DIFFRACTIONf_plane_restr0.0072740
X-RAY DIFFRACTIONf_dihedral_angle_d13.3678943
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A7556X-RAY DIFFRACTION12.247TORSIONAL
12B7556X-RAY DIFFRACTION12.247TORSIONAL
13C7556X-RAY DIFFRACTION12.247TORSIONAL
14D7556X-RAY DIFFRACTION12.247TORSIONAL
15E7556X-RAY DIFFRACTION12.247TORSIONAL
16F7556X-RAY DIFFRACTION12.247TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.45580.31151320.25755702583499
2.4558-2.51720.30261360.23635715585199
2.5172-2.58520.29371300.23745678580899
2.5852-2.66130.32071460.2325698584499
2.6613-2.74720.28121500.22165699584999
2.7472-2.84540.28031350.22845750588599
2.8454-2.95930.28781420.22615661580399
2.9593-3.09390.28671230.21025715583899
3.0939-3.2570.25911350.21285732586799
3.257-3.4610.26391340.20715693582799
3.461-3.72810.23431300.18315715584599
3.7281-4.10310.21031320.165714584699
4.1031-4.69630.16321290.13685773590299
4.6963-5.91490.18151440.15045745588999
5.9149-46.13190.19151430.15065803594698
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)
11.96030.5205-0.90065.2656-1.66312.7948-0.1572-0.28660.14930.49080.28890.2024-0.8269-0.1051-0.20210.7650.1182-0.02940.4329-0.06360.3253-43.90319.849332.781
22.0171-0.2929-0.63433.83320.87483.9874-0.0666-0.1497-0.11020.26710.13330.0928-0.08590.0087-0.05810.36850.0352-0.05430.27360.02020.3535-43.97985.814624.618
33.4661-2.03631.86571.8239-1.16553.0767-0.0999-0.25430.06260.0962-0.0087-0.2322-0.1520.54910.11730.5309-0.0018-0.05740.49630.01030.4209-24.726610.82931.6127
42.08221.20610.12692.01240.05754.6605-0.15290.122-0.0493-0.14220.16230.09240.9142-0.3647-0.03130.5648-0.0904-0.01630.30470.03930.4029-56.1663-21.09036.2383
52.22240.8921-0.01784.48570.13134.2208-0.21520.19450.3471-0.45690.14140.0295-0.24270.01770.0780.3705-0.0206-0.0720.27040.00030.3351-46.7219-6.65838.8345
62.6617-0.12830.44153.8381-2.32775.07830.09670.39890.4628-0.4370.40590.59120.0114-0.5532-0.42570.4963-0.04410.01250.40850.10650.5226-56.2635-7.0353-11.6483
71.87381.1654-0.0915.0101-1.27394.5286-0.153-0.25220.2870.69030.17970.2414-0.3935-0.55120.03920.46140.11390.17390.43280.01070.4728-66.017446.132669.5188
85.9657-0.3338-1.5241.3137-0.21074.44380.22470.24990.90840.14450.02180.0376-0.71570.0899-0.25820.495-0.02150.01710.30310.04830.4937-54.887753.732659.155
94.85150.102-0.44814.1431.5573.6147-0.08570.5297-0.6706-0.16340.1565-0.14990.27070.10790.00870.41260.0413-0.01660.51050.00730.3975-53.753334.217457.973
105.2708-0.3685-1.34873.64890.55672.88140.23730.2301-0.39260.20850.1794-0.19060.01960.0662-0.18030.36330.0026-0.00970.39070.01420.3451-47.518140.835761.174
115.47070.4529-1.35032.5496-0.12610.3744-0.0034-0.3043-0.0810.415-0.13320.1007-0.0039-0.05780.20130.33120.09270.01610.30650.03610.285-57.424241.977365.1895
122.2753-1.2782.60683.2697-2.00339.8550.03280.4741-0.0441-0.2858-0.0208-0.0450.0280.12410.06020.40880.0432-0.06150.65430.0810.5485-71.191445.373539.5748
134.9711-1.84454.7310.832-1.91334.63530.72230.7837-0.4152-1.23-0.46340.24530.51650.7804-0.12340.950.1695-0.06830.6815-0.04520.5784-69.437633.227536.6797
142.2212-0.92812.69482.4731-2.07829.01710.31330.4318-0.2976-0.44740.00990.3640.9383-0.0835-0.27570.3852-0.02430.0440.42840.00420.4565-68.938834.317551.1223
152.2657-1.21981.98461.3891-2.14246.2938-0.01090.1396-0.1660.20130.34360.4523-0.0863-0.7391-0.26520.37260.01880.05590.5150.09050.5104-74.535941.010553.45
161.08160.04960.22372.63440.33991.94230.00440.76450.0302-0.24510.3648-0.7892-0.12551.1183-0.36480.6024-0.22110.02021.5888-0.10570.6777-17.971345.10244.5802
178.36530.7095-5.96862.9533-0.55434.38640.17590.46020.9625-0.0366-0.0107-0.2384-0.82211.5626-0.34150.6118-0.337-0.03471.34840.09790.5869-25.05753.234853.044
184.51010.51811.00481.49010.29052.94370.1120.8619-0.28760.02980.0335-0.32280.19090.8194-0.16150.41550.0048-0.0520.7895-0.09970.4051-35.249840.124453.0225
195.01890.03251.56391.41760.85661.34760.451.2311-0.0920.33360.0997-0.24720.48491.164-0.27270.55470.0748-0.06430.998-0.2050.6073-21.978139.70255.8585
202.59190.60712.16821.4702-0.00684.53960.4091.0026-0.88170.21720.0946-0.31490.73910.7406-0.49440.74060.3079-0.21521.2116-0.44360.9064-14.53729.200158.6753
211.65021.3160.40184.33241.90155.46880.5161.2898-0.31860.14760.3884-0.7059-0.07731.13090.11750.69430.1965-0.36521.2986-0.31030.7234-6.10838.262864.3509
223.5536-3.0977-0.84212.8040.70593.2737-0.2658-0.2463-0.68440.1486-0.352-0.40670.82490.23480.74660.8354-0.1401-0.11480.72070.35440.7542-1.5125-20.24191.504
233.0035-1.30990.62033.2498-0.64882.68960.49710.0422-0.602-0.0761-0.7266-0.47471.240.72890.51890.86510.0337-0.06640.6970.16440.8711.1518-19.2995-11.0728
241.4375-0.80950.61644.1053-1.37483.59950.166-0.4014-0.06470.3892-0.4912-0.5343-0.14120.03530.29310.4674-0.0992-0.16730.77330.13310.6204-3.1262-3.3215-6.3787
252.7204-0.56420.90083.0141-0.8984.26920.038-0.554-0.4220.3153-0.2419-0.1184-0.0106-0.30810.11390.4974-0.0653-0.14510.81840.14670.5603-9.0102-4.4528-5.5144
260.78712.05251.13785.72223.25941.87080.15740.28-0.80940.35610.6701-0.26780.3353-0.2974-0.90350.7986-0.1699-0.33941.3440.36361.012619.3935-4.42354.9483
278.57466.86412.52535.6691.44183.1586-0.1559-1.91891.1837-0.6014-0.2797-0.60930.3159-0.28090.59870.96330.1594-0.18931.12230.00461.366617.255.459212.3311
285.19361.74381.40553.03831.98331.74070.0657-1.5114-1.28650.6092-0.2275-0.87870.4221-0.294-0.13430.8795-0.2467-0.22271.20710.52540.8445-1.4884-13.8188.4762
296.5336-1.24842.07491.22080.78782.18330.0245-1.14761.18921.2477-0.6944-0.3393-1.5141-0.26070.49571.1702-0.5161-0.40221.30920.30650.74040.6849-3.273812.123
300.3107-0.4321-0.20710.8710.37370.1328-0.7667-0.3990.14290.17380.4993-0.19160.1545-0.38480.35630.9381-0.3163-0.21661.45290.29640.75320.9692-7.571615.5022
312.4277-0.3664-0.14420.78190.87354.3083-0.2284-0.4698-0.72230.562-0.5733-0.48140.1941-0.03880.08190.7775-0.076-0.37381.21740.6391.296418.5005-12.0437.504
322.1352-0.0552-0.0922.6326-0.33756.1270.01910.08390.2464-0.2635-0.1893-0.3166-0.25570.78510.15740.39440.06270.00760.49910.04150.4066-8.02819.3865-35.806
333.11421.00591.6985.1602-1.80354.5464-0.01370.3323-0.1042-0.45010.0112-0.07040.12140.25010.00670.43740.11960.00350.5883-0.03460.4659-6.50737.5665-34.6062
341.9421-0.60171.63714.4504-1.16072.6465-0.0563-0.17840.01360.5478-0.1215-0.1132-0.2117-0.45530.22170.42390.0812-0.11720.68110.01280.4389-9.975710.1039-17.7325
359.68292.1147-1.98935.5557-2.07426.34410.1583-0.76730.18930.4428-0.1323-0.2519-0.2147-0.1450.07630.51070.1173-0.1540.65220.02320.4961-5.03799.276-15.5691
367.43890.54691.32421.6124-0.10731.5802-0.3287-0.2983-0.34040.06140.06480.01710.10970.0220.24980.49080.08210.02710.30920.00730.3793-25.138312.2208-28.0161
378.35623.70253.10343.21161.77014.24040.7875-0.835-0.21151.352-0.57980.3081.2378-0.3943-0.02940.7649-0.1120.08050.4424-0.03580.545-38.370914.9276-19.5732
386.45541.0325-0.93282.76710.43692.37530.0448-0.45870.25110.52690.0275-0.1686-0.08770.4997-0.1240.53160.0727-0.03320.3386-0.01770.3784-20.666123.2064-24.9137
392.94160.788-0.05982.78850.86522.80010.1406-0.12780.01440.5446-0.11190.10210.0887-0.0281-0.01670.53670.0805-0.02460.34320.00450.4498-29.522219.6296-26.7104
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 38 )A0 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 171 )A39 - 171
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 333 )A172 - 333
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 68 )B4 - 68
5X-RAY DIFFRACTION5chain 'B' and (resid 69 through 171 )B69 - 171
6X-RAY DIFFRACTION6chain 'B' and (resid 172 through 333 )B172 - 333
7X-RAY DIFFRACTION7chain 'C' and (resid 0 through 38 )C0 - 38
8X-RAY DIFFRACTION8chain 'C' and (resid 39 through 110 )C39 - 110
9X-RAY DIFFRACTION9chain 'C' and (resid 111 through 144 )C111 - 144
10X-RAY DIFFRACTION10chain 'C' and (resid 145 through 170 )C145 - 170
11X-RAY DIFFRACTION11chain 'C' and (resid 171 through 186 )C171 - 186
12X-RAY DIFFRACTION12chain 'C' and (resid 187 through 213 )C187 - 213
13X-RAY DIFFRACTION13chain 'C' and (resid 214 through 228 )C214 - 228
14X-RAY DIFFRACTION14chain 'C' and (resid 229 through 298 )C229 - 298
15X-RAY DIFFRACTION15chain 'C' and (resid 299 through 333 )C299 - 333
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 38 )D1 - 38
17X-RAY DIFFRACTION17chain 'D' and (resid 39 through 89 )D39 - 89
18X-RAY DIFFRACTION18chain 'D' and (resid 90 through 170 )D90 - 170
19X-RAY DIFFRACTION19chain 'D' and (resid 171 through 198 )D171 - 198
20X-RAY DIFFRACTION20chain 'D' and (resid 199 through 312 )D199 - 312
21X-RAY DIFFRACTION21chain 'D' and (resid 313 through 333 )D313 - 333
22X-RAY DIFFRACTION22chain 'E' and (resid 5 through 38 )E5 - 38
23X-RAY DIFFRACTION23chain 'E' and (resid 39 through 68 )E39 - 68
24X-RAY DIFFRACTION24chain 'E' and (resid 69 through 144 )E69 - 144
25X-RAY DIFFRACTION25chain 'E' and (resid 145 through 186 )E145 - 186
26X-RAY DIFFRACTION26chain 'E' and (resid 187 through 213 )E187 - 213
27X-RAY DIFFRACTION27chain 'E' and (resid 214 through 228 )E214 - 228
28X-RAY DIFFRACTION28chain 'E' and (resid 229 through 245 )E229 - 245
29X-RAY DIFFRACTION29chain 'E' and (resid 246 through 274 )E246 - 274
30X-RAY DIFFRACTION30chain 'E' and (resid 275 through 312 )E275 - 312
31X-RAY DIFFRACTION31chain 'E' and (resid 313 through 333 )E313 - 333
32X-RAY DIFFRACTION32chain 'F' and (resid 5 through 38 )F5 - 38
33X-RAY DIFFRACTION33chain 'F' and (resid 39 through 89 )F39 - 89
34X-RAY DIFFRACTION34chain 'F' and (resid 90 through 144 )F90 - 144
35X-RAY DIFFRACTION35chain 'F' and (resid 145 through 171 )F145 - 171
36X-RAY DIFFRACTION36chain 'F' and (resid 172 through 213 )F172 - 213
37X-RAY DIFFRACTION37chain 'F' and (resid 214 through 228 )F214 - 228
38X-RAY DIFFRACTION38chain 'F' and (resid 229 through 274 )F229 - 274
39X-RAY DIFFRACTION39chain 'F' and (resid 275 through 333 )F275 - 333

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万見について

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お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る