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- PDB-9hde: Crystal structure of methionine gamma-lyase (K209Q variant) from ... -

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基本情報

登録情報
データベース: PDB / ID: 9hde
タイトルCrystal structure of methionine gamma-lyase (K209Q variant) from Brevibacterium aurantiacum in complex with PLP and alpha-ketobutyrate
要素Cystathionine gamma-synthase
キーワードLYASE / Complex / inhibitor / methionine / PLP
機能・相同性
機能・相同性情報


homocysteine desulfhydrase / methionine gamma-lyase / methionine gamma-lyase activity / cystathionine gamma-lyase activity / cysteine biosynthetic process via cystathionine / transsulfuration / pyridoxal phosphate binding / cytoplasm
類似検索 - 分子機能
Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
類似検索 - ドメイン・相同性
Chem-4LM / DI(HYDROXYETHYL)ETHER / L-methionine gamma-lyase
類似検索 - 構成要素
生物種Brevibacterium aurantiacum (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: 2.522 Å
データ登録者Kopecny, D. / Ferchaud, N. / Briozzo, P.
資金援助 チェコ, フランス, 4件
組織認可番号国
Ministry of Education, Youth and Sports of the Czech RepublicMOBILITY 8J23FR011 チェコ
Other governmentFR 49271QH PHC BARRANDE
Agence Nationale de la Recherche (ANR)France 2023 ANR-11-IDEX-0003, Jean d'Alembert fellowship at Paris-Saclay フランス
Other privateIMEBATRACA
引用ジャーナル: To Be Published
タイトル: Functional and structural characterization of methionine gamma-lyases from Brevibacterium bacteria: insights into cofactor retention
著者: Ferchaud, N. / Boyer, A. / Odegard, B. / Hentati, S. / Simonson, T. / Machover, D. / Kopecny, D. / Briozzo, P.
履歴
登録2024年11月12日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02025年10月22日Provider: repository / タイプ: Initial release

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Cystathionine gamma-synthase
B: Cystathionine gamma-synthase
C: Cystathionine gamma-synthase
D: Cystathionine gamma-synthase
E: Cystathionine gamma-synthase
F: Cystathionine gamma-synthase
G: Cystathionine gamma-synthase
H: Cystathionine gamma-synthase
I: Cystathionine gamma-synthase
J: Cystathionine gamma-synthase
K: Cystathionine gamma-synthase
L: Cystathionine gamma-synthase
M: Cystathionine gamma-synthase
N: Cystathionine gamma-synthase
O: Cystathionine gamma-synthase
P: Cystathionine gamma-synthase
Q: Cystathionine gamma-synthase
R: Cystathionine gamma-synthase
S: Cystathionine gamma-synthase
T: Cystathionine gamma-synthase
U: Cystathionine gamma-synthase
V: Cystathionine gamma-synthase
W: Cystathionine gamma-synthase
X: Cystathionine gamma-synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,037,77670
ポリマ－1,027,66624
非ポリマー10,10946
水7,746430
1
A: Cystathionine gamma-synthase
B: Cystathionine gamma-synthase
C: Cystathionine gamma-synthase
D: Cystathionine gamma-synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)173,59918
ポリマ－171,2784
非ポリマー2,32214
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area20900 Å2
ΔGint-187 kcal/mol
Surface area43820 Å2
手法PISA
2
E: Cystathionine gamma-synthase
F: Cystathionine gamma-synthase
G: Cystathionine gamma-synthase
H: Cystathionine gamma-synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)172,89711
ポリマ－171,2784
非ポリマー1,6197
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area19610 Å2
ΔGint-151 kcal/mol
Surface area43860 Å2
手法PISA
3
I: Cystathionine gamma-synthase
J: Cystathionine gamma-synthase
K: Cystathionine gamma-synthase
L: Cystathionine gamma-synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)172,79110
ポリマ－171,2784
非ポリマー1,5136
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area19250 Å2
ΔGint-151 kcal/mol
Surface area44080 Å2
手法PISA
4
M: Cystathionine gamma-synthase
N: Cystathionine gamma-synthase
O: Cystathionine gamma-synthase
P: Cystathionine gamma-synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)173,08913
ポリマ－171,2784
非ポリマー1,8119
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area19920 Å2
ΔGint-173 kcal/mol
Surface area44140 Å2
手法PISA
5
Q: Cystathionine gamma-synthase
R: Cystathionine gamma-synthase
S: Cystathionine gamma-synthase
T: Cystathionine gamma-synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)172,5998
ポリマ－171,2784
非ポリマー1,3214
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area19210 Å2
ΔGint-131 kcal/mol
Surface area43740 Å2
手法PISA
6
U: Cystathionine gamma-synthase
V: Cystathionine gamma-synthase
W: Cystathionine gamma-synthase
X: Cystathionine gamma-synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)172,80110
ポリマ－171,2784
非ポリマー1,5236
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area19400 Å2
ΔGint-144 kcal/mol
Surface area43800 Å2
手法PISA
単位格子
Length a, b, c (Å)133.328, 155.89, 232.079
Angle α, β, γ (deg.)90, 90.24, 90
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質 ...
Cystathionine gamma-synthase / Methionine gamma-lyase (MGL)


分子量: 42819.430 Da / 分子数: 24 / 由来タイプ: 組換発現 / 詳細: N-terminal His-tag, mutation K209Q
由来: (組換発現) Brevibacterium aurantiacum (バクテリア)
遺伝子: BAUR9175_03070, BAUR920_03040, BAURA63_02933, BAURA86_00394
発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): T7 express / 参照: UniProt: A0A2H1K3G9, methionine gamma-lyase
#2: 化合物
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


分子量: 106.120 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C4H10O3
#3: 化合物
ChemComp-SO4 / SULFATE ION


分子量: 96.063 Da / 分子数: 15 / 由来タイプ: 合成 / 式: SO4
#4: 化合物...
ChemComp-4LM / (2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid


分子量: 330.230 Da / 分子数: 24 / 由来タイプ: 合成 / 式: C12H15N2O7P / タイプ: SUBJECT OF INVESTIGATION
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 430 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY
Has protein modificationN

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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: 2.48 Å3/Da / 溶媒含有率: 47.59 %
結晶化温度: 294 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5
詳細: Well solution 0.1 M Tris-HCl, pH 8.5, 0.1 M Lithium sulfate, 32% PEG4000, 1 mM PLP, 20 mM Methionine, Cryoprotection: 10% PEG400

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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: SOLEIL / ビームライン: PROXIMA 2 / 波長: 0.98399 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2023年3月29日
詳細: a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
放射モノクロメーター: Cryogenically cooled channel cut crystal monochromator
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: 0.98399 Å / 相対比: 1
反射解像度: 2.522→232.077 Å / Num. obs: 214191 / % possible obs: 93.6 % / 冗長度: 6.32 %
詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.98 / CC1/2 anomalous: -0.043 / Rmerge(I) obs: 0.3218 / Rpim(I) all: 0.1356 / Rrim(I) all: 0.3498 / AbsDiff over sigma anomalous: 0.773 / Baniso tensor eigenvalue 1: 33.7 Å2 / Baniso tensor eigenvalue 2: 54.6 Å2 / Baniso tensor eigenvalue 3: 37 Å2 / Baniso tensor eigenvector 1 ortho1: 0.9167 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: -0.3996 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0.3996 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.9167 / Aniso diffraction limit 1: 2.852 Å / Aniso diffraction limit 2: 3.152 Å / Aniso diffraction limit 3: 2.522 Å / Aniso diffraction limit axis 1 ortho1: 0.90493 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0.42547 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: -0.42547 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.90493 / Net I/σ(I): 5.9 / Num. measured all: 1354142 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 93.2 / % possible ellipsoidal: 93.6 / % possible ellipsoidal anomalous: 93.2 / % possible spherical: 67.2 / % possible spherical anomalous: 66.5 / Redundancy anomalous: 3.21 / Signal type: local
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
7.857-232.0776.310.068116.72675366753610709107090.996-0.3240.02930.07430.62297.899.297.899.297.83.399.2
6.228-7.8576.020.118711.43644676446710710107100.993-0.1750.05130.12960.73198.999.998.999.998.93.0999.9
5.438-6.2286.350.16039.87679626796210710107100.988-0.0950.06740.17420.7599.699.999.699.999.63.2399.9
4.938-5.4386.270.17739.33671176711710709107090.985-0.1080.07550.19310.76998.999.998.999.998.93.299.9
4.582-4.9385.730.17169.34613646136410712107120.984-0.0830.07660.18840.7897.999.997.999.997.92.9499.9
4.31-4.5826.170.19578.95660866608610706107060.982-0.0840.08370.21320.77599.399.999.399.999.33.1499.9
4.093-4.316.350.22668.07680616806110711107110.976-0.0740.09510.24620.76999.799.999.799.999.73.2299.9
3.914-4.0936.410.27817686576865710709107090.964-0.0540.1160.30170.78199.899.999.899.999.83.2599.9
3.763-3.9146.470.30686.38692516925110709107090.959-0.0360.1270.33240.78499.799.999.799.999.73.2799.9
3.632-3.7636.520.36125.57698276982710709107090.947-0.0270.1490.39120.78499.899.999.899.999.83.399.9
3.518-3.6326.560.46144.49702457024510709107090.916-0.0290.18950.49940.78699.999.899.999.899.93.3199.8
3.417-3.5186.580.53963.87704487044810711107110.881-0.0170.22170.5840.79199.799.899.799.899.73.3299.8
3.326-3.4176.60.67753.12707377073710710107100.850.0030.27840.73320.79399.899.899.899.899.83.3399.8
3.244-3.3266.160.73962.7659806598010710107100.7730.0010.31750.80630.79499.899.899.899.899.83.1199.8
3.17-3.2445.850.81952.34626976269710709107090.691-0.0240.36310.89830.78598.498.898.498.898.42.9698.8
3.095-3.1696.270.96352.1671756717510710107100.621-0.0070.41051.04880.78891.591.991.589.889.43.1791.9
3.015-3.0956.461.12841.81691776917710709107090.5590.0030.47291.2250.79585.886.385.876.976.43.2786.3
2.929-3.0156.531.2271.67699616996110710107100.5020.0010.51121.33090.78881.381.781.363.162.43.3181.7
2.82-2.9296.561.24031.64702397023910709107090.48-0.0110.5141.34440.78675.576.175.543.8433.3476.1
2.522-2.826.271.21921.63671556715510710107100.44-0.0090.51621.32630.79461.561.661.511.911.53.261.6

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解析

ソフトウェア
名称バージョン分類
MxCuBEデータ収集
autoPROC1.0.5data processing
XDSJan 10, 2022データ削減
Aimless0.7.7データスケーリング
STARANISO2.3.79データスケーリング
Coot0.9.8モデル構築
BUSTER2.10.4精密化
PHASER2.7位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.522→232.08 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.876 / 交差検証法: THROUGHOUT / SU Rfree Blow DPI: 0.413
Rfactor反射数%反射Selection details
Rfree0.2652 10624 -RANDOM
Rwork0.2577 ---
obs0.2581 214191 67.2 %-
原子変位パラメータBiso mean: 59.77 Å2
Baniso -1Baniso -2Baniso -3
1-1.2175 Å20 Å22.9363 Å2
2---3.5211 Å20 Å2
3---2.3036 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
精密化ステップサイクル: LAST / 解像度: 2.522→232.08 Å
タンパク質核酸リガンド溶媒全体
原子数67475 0 652 430 68557
拘束条件
Refine-IDタイプDev ideal数Restraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.008136785HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.96247597HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d40701SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes23192HARMONIC5
X-RAY DIFFRACTIONt_it136785HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion9303SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact111694SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.39
X-RAY DIFFRACTIONt_other_torsion15.47
LS精密化 シェル解像度: 2.522→2.71 Å
Rfactor反射数%反射
Rfree0.3368 178 -
Rwork0.3399 --
obs--6.84 %
精密化 TLS

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)
11.2120.3061-0.12571.05070.28210.30140.3450.01380.01930.0138-0.27380.0930.01930.093-0.0711-0.2327-0.18630.18880.26-0.30480.0128-11.6722-3.269741.2098
20.4578-0.1395-0.17931.22240.30592.35070.00620.35940.55040.3594-0.0798-0.0230.5504-0.0230.07360.2039-0.10550.05330.11250.0673-0.244212.242741.8221106.8833
31.78420.46780.41320.94420.25430.38110.0295-0.1276-0.1455-0.1276-0.0555-0.2375-0.1455-0.23750.0260.06210.04770.1101-0.24380.03090.121255.7682-2.44089.2407
41.62440.2618-0.69221.0094-0.05392.0954-0.70180.19790.60190.19790.3692-0.02520.6019-0.02520.33260.1729-0.04030.2241-0.098-0.1293-0.036550.9253-33.083683.0464
51.06550.39230.2931.043-0.06290.6260.1114-0.13960.0828-0.1396-0.0604-0.05560.0828-0.0556-0.0510.0104-0.00480.037-0.1957-0.05340.18655.0864-34.65729.6609
61.36510.6636-0.3041.2669-0.1470.63020.00510.11690.09210.1169-0.1260.35690.09210.35690.1209-0.010.0320.0624-0.10940.00920.16754.736144.688332.975
71.77690.5105-0.6520.9416-0.26741.18540.24940.185-0.24140.1850.0665-0.31-0.2414-0.31-0.31590.06860.06210.1809-0.1885-0.02440.211815.558273.681231.9491
81.28420.12450.0831.26710.340.8550.26850.1710.04840.171-0.0391-0.18150.0484-0.1815-0.2294-0.0151-0.17-0.1106-0.12040.1870.171173.6738-34.614841.0822
91.74510.3482-0.01772.22170.48011.4937-0.06860.18020.73830.18020.27830.63240.73830.6324-0.2096-0.11670.2306-0.16780.2185-0.303-0.198178.745648.939174.6079
101.4480.081-0.0061.046-0.21340.7274-0.0884-0.0460.2118-0.0460.069-0.33680.2118-0.33680.01940.0801-0.10430.0956-0.127-0.0190.05618.529541.203133.1305
111.82730.1939-0.21460.9717-0.13060.3141-0.5609-0.00820.3914-0.00820.3491-0.42470.3914-0.42470.21180.0045-0.30420.28360.20590.0474-0.19514.5585-36.45184.1675
121.2731-0.08950.08070.6637-0.29291.54820.17030.12-0.58360.12-0.12980.0679-0.58360.0679-0.04040.3327-0.05360.15230.0967-0.1886-0.24197.241173.8691105.6927
131.9658-0.1296-0.72190.820.24680.356-0.34790.249-0.11260.2490.3729-0.5397-0.1126-0.5397-0.025-0.10340.0129-0.00360.34570.2659-0.18111.6626-4.14483.4455
142.69120.40650.13480.86190.10880.20550.14340.04480.03910.0448-0.11270.15920.03910.1592-0.0307-0.02750.0032-0.0038-0.1355-0.16560.21756.3854-36.0539.8316
150.06890.35020.33621.41330.5122.23130.0026-0.0426-0.2243-0.04260.23090.3456-0.22430.3456-0.2335-0.1184-0.20390.01340.3042-0.1062-0.035875.103281.190875.9997
161.4536-0.152-0.38411.08040.15550.51870.0670.17990.53870.17990.0818-0.09150.5387-0.0915-0.14880.39060.0639-0.2272-0.0292-0.0608-0.222860.994945.4958106.4011
171.94340.0242-0.75410.7218-0.25931.583-0.23090.0089-0.24990.00890.3194-0.0196-0.2499-0.0196-0.08850.074-0.0651-0.0938-0.0697-0.02390.023648.0173-0.802883.4792
180.7592-0.0090.20271.1424-0.16651.85120.10610.3549-0.34890.35490.04790.0338-0.34890.0338-0.1540.13270.0207-0.06460.0946-0.0832-0.137156.277377.8649107.1587
191.45740.07010.36670.8848-0.09860.2020.12740.0506-0.10420.0506-0.02080.0788-0.10420.0788-0.10670.0407-0.13020.08910.0005-0.10940.091873.3455-2.187541.1391
200.23080.04390.25961.89330.40271.73830.0466-0.0962-0.808-0.0962-0.1464-0.9914-0.808-0.99140.09980.02890.30450.10580.2824-0.1305-0.2154-9.743570.284273.4815
212.06840.43050.00831.08090.33490.55740.1646-0.0846-0.0482-0.0846-0.0905-0.0715-0.0482-0.0715-0.0741-0.04650.00160.099-0.08910.01880.21497.0407-3.61219.8718
222.4009-0.0967-0.0690.91840.09790.65270.2636-0.15530.0243-0.1553-0.1954-0.20980.0243-0.2098-0.0682-0.219-0.26660.00450.28610.23620.0448-11.265-35.756441.7133
230.22160.3461-0.08251.4530.17321.98610.08830.0590.29020.059-0.2002-0.53120.2902-0.53120.11190.0635-0.21020.09760.2306-0.068-0.1597-5.986837.706375.4746
241.18010.2392-0.56281.0863-0.43090.93110.28810.0758-0.40260.0758-0.11470.3762-0.40260.3762-0.17340.125-0.19340.1318-0.1566-0.10140.082951.910776.898832.9257
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ E|* }E2 - 389
2X-RAY DIFFRACTION1{ E|* }E395
3X-RAY DIFFRACTION1{ E|* }E396 - 410
4X-RAY DIFFRACTION2{ T|* }T4 - 389
5X-RAY DIFFRACTION2{ T|* }T395
6X-RAY DIFFRACTION2{ T|* }T396 - 400
7X-RAY DIFFRACTION3{ B|* }B3 - 389
8X-RAY DIFFRACTION3{ B|* }B395 - 398
9X-RAY DIFFRACTION3{ B|* }B399 - 445
10X-RAY DIFFRACTION3{ B|* }B446
11X-RAY DIFFRACTION3{ B|* }B448 - 450
12X-RAY DIFFRACTION4{ K|* }K3 - 389
13X-RAY DIFFRACTION4{ K|* }K395
14X-RAY DIFFRACTION4{ K|* }K396 - 404
15X-RAY DIFFRACTION5{ A|* }A3 - 389
16X-RAY DIFFRACTION5{ A|* }A395 - 399
17X-RAY DIFFRACTION5{ A|* }A400 - 446
18X-RAY DIFFRACTION6{ P|* }P2 - 389
19X-RAY DIFFRACTION6{ P|* }P395 - 396
20X-RAY DIFFRACTION6{ P|* }P397 - 417
21X-RAY DIFFRACTION6{ P|* }P418
22X-RAY DIFFRACTION7{ N|* }N2 - 389
23X-RAY DIFFRACTION7{ N|* }N395 - 396
24X-RAY DIFFRACTION7{ N|* }N397 - 419
25X-RAY DIFFRACTION7{ N|* }N420
26X-RAY DIFFRACTION8{ D|* }D3 - 389
27X-RAY DIFFRACTION8{ D|* }D395 - 396
28X-RAY DIFFRACTION8{ D|* }D397 - 422
29X-RAY DIFFRACTION9{ W|* }W3 - 388
30X-RAY DIFFRACTION9{ W|* }W395
31X-RAY DIFFRACTION9{ W|* }W396 - 398
32X-RAY DIFFRACTION10{ M|* }M2 - 389
33X-RAY DIFFRACTION10{ M|* }M395 - 396
34X-RAY DIFFRACTION10{ M|* }M398 - 438
35X-RAY DIFFRACTION11{ J|* }J3 - 389
36X-RAY DIFFRACTION11{ J|* }J395 - 396
37X-RAY DIFFRACTION11{ J|* }J397 - 402
38X-RAY DIFFRACTION12{ S|* }S2 - 389
39X-RAY DIFFRACTION12{ S|* }S395
40X-RAY DIFFRACTION12{ S|* }S396 - 402
41X-RAY DIFFRACTION13{ I|* }I2 - 388
42X-RAY DIFFRACTION13{ I|* }I395
43X-RAY DIFFRACTION13{ I|* }I396 - 401
44X-RAY DIFFRACTION14{ G|* }G3 - 389
45X-RAY DIFFRACTION14{ G|* }G395
46X-RAY DIFFRACTION14{ G|* }G396 - 428
47X-RAY DIFFRACTION15{ X|* }X2 - 388
48X-RAY DIFFRACTION15{ X|* }X395
49X-RAY DIFFRACTION15{ X|* }X396 - 397
50X-RAY DIFFRACTION16{ V|* }V4 - 388
51X-RAY DIFFRACTION16{ V|* }V395 - 396
52X-RAY DIFFRACTION16{ V|* }V397 - 399
53X-RAY DIFFRACTION17{ L|* }L2 - 389
54X-RAY DIFFRACTION17{ L|* }L395 - 396
55X-RAY DIFFRACTION17{ L|* }L397 - 404
56X-RAY DIFFRACTION18{ U|* }U3 - 389
57X-RAY DIFFRACTION18{ U|* }U395
58X-RAY DIFFRACTION18{ U|* }U396 - 400
59X-RAY DIFFRACTION19{ C|* }C3 - 389
60X-RAY DIFFRACTION19{ C|* }C395 - 396
61X-RAY DIFFRACTION19{ C|* }C397 - 425
62X-RAY DIFFRACTION20{ R|* }R3 - 389
63X-RAY DIFFRACTION20{ R|* }R395
64X-RAY DIFFRACTION20{ R|* }R396 - 399
65X-RAY DIFFRACTION21{ H|* }H3 - 389
66X-RAY DIFFRACTION21{ H|* }H395 - 397
67X-RAY DIFFRACTION21{ H|* }H398 - 431
68X-RAY DIFFRACTION22{ F|* }F2 - 388
69X-RAY DIFFRACTION22{ F|* }F395 - 396
70X-RAY DIFFRACTION22{ F|* }F397 - 410
71X-RAY DIFFRACTION23{ Q|* }Q2 - 389
72X-RAY DIFFRACTION23{ Q|* }Q395
73X-RAY DIFFRACTION23{ Q|* }Q396 - 408
74X-RAY DIFFRACTION24{ O|* }O2 - 389
75X-RAY DIFFRACTION24{ O|* }O395 - 396
76X-RAY DIFFRACTION24{ O|* }O397 - 424

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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