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- PDB-3zp4: Arg90Cit chorismate mutase of Bacillus subtilis in complex with a... -

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基本情報

登録情報
データベース: PDB / ID: 3zp4
タイトルArg90Cit chorismate mutase of Bacillus subtilis in complex with a transition state analog
要素CHORISMATE MUTASE AROH
キーワードISOMERASE / PSEUDO-ALPHA BETA-BARREL / NON-PROTEINOGENIC AMINO ACID / SEMI-SYNTHETIC / TRANSITION STATE ANALOG
機能・相同性
機能・相同性情報


chorismate metabolic process / chorismate mutase / chorismate mutase activity / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytoplasm
類似検索 - 分子機能
Chorismate mutase, AroH class / Chorismate mutase type I / Chorismate mutase domain profile. / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Chem-TSA / Chorismate mutase AroH
類似検索 - 構成要素
生物種BACILLUS SUBTILIS (枯草菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.798 Å
データ登録者Burschowsky, D. / vanEerde, A. / Okvist, M. / Kienhofer, A. / Kast, P. / Hilvert, D. / Krengel, U.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / : 2014
タイトル: Electrostatic Transition State Stabilization Rather Than Reactant Destabilization Provides the Chemical Basis for Efficient Chorismate Mutase Catalysis.
著者: Burschowsky, D. / Van Eerde, A. / Okvist, M. / Kienhofer, A. / Kast, P. / Hilvert, D. / Krengel, U.
履歴
登録2013年2月26日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02014年4月16日Provider: repository / タイプ: Initial release
改定 1.12014年11月26日Group: Database references
改定 1.22014年12月3日Group: Database references
改定 1.32014年12月10日Group: Database references
改定 1.42014年12月24日Group: Database references
改定 2.02023年11月15日Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
改定 2.12023年12月20日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model
改定 2.22024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: CHORISMATE MUTASE AROH
B: CHORISMATE MUTASE AROH
C: CHORISMATE MUTASE AROH
D: CHORISMATE MUTASE AROH
E: CHORISMATE MUTASE AROH
F: CHORISMATE MUTASE AROH
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)88,04410
ポリマ-87,1326
非ポリマー9134
6,413356
1
A: CHORISMATE MUTASE AROH
B: CHORISMATE MUTASE AROH
C: CHORISMATE MUTASE AROH
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,0225
ポリマ-43,5663
非ポリマー4562
543
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-17.4 kcal/mol
Surface area14440 Å2
手法PISA
2
D: CHORISMATE MUTASE AROH
E: CHORISMATE MUTASE AROH
F: CHORISMATE MUTASE AROH
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,0225
ポリマ-43,5663
非ポリマー4562
543
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-17.4 kcal/mol
Surface area14450 Å2
手法PISA
単位格子
Length a, b, c (Å)50.208, 50.842, 69.821
Angle α, β, γ (deg.)97.36, 93.18, 100.99
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
CHORISMATE MUTASE AROH / CHORISMATE MUTASE / CM


分子量: 14521.919 Da / 分子数: 6 / 変異: YES / 由来タイプ: 組換発現 / 由来: (組換発現) BACILLUS SUBTILIS (枯草菌) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: P19080
#2: 化合物
ChemComp-TSA / 8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID / (1R,5S)-2-オキサ-8β-ヒドロキシビシクロ[3.3.1]ノナ-6-エン-3α,5-ジカルボン酸


分子量: 228.199 Da / 分子数: 4 / 由来タイプ: 合成 / : C10H12O6
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 356 / 由来タイプ: 天然 / : H2O
Has protein modificationY

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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: 2.25 Å3/Da / 溶媒含有率: 45.38 % / 解説: NONE
結晶化pH: 6
詳細: 100 MM MMT BUFFER - MALIC ACID, MES, TRIS, IN MOLAR RATIOS OF 1:2:2, RESPECTIVELY - PH 6.0, 125 MM CALCIUM CHLORIDE, 24% W/V PEG 1000

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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: ESRF / ビームライン: ID23-2 / 波長: 0.8726
検出器検出器: CCD / 日付: 2011年10月2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: 0.8726 Å / 相対比: 1
反射解像度: 1.8→49.12 Å / Num. obs: 53585 / % possible obs: 86.1 % / 冗長度: 1.9 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 23.3
反射 シェル解像度: 1.8→1.9 Å / 冗長度: 1.8 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5 / % possible all: 61.8

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 1DBF
解像度: 1.798→43.167 Å / SU ML: 0.24 / σ(F): 1.97 / 位相誤差: 26.62 / 立体化学のターゲット値: ML
詳細: INITIAL REFINEMENTS WERE PERFORMED WITH REFMAC. FINAL REFINEMENT WAS PERFORMED WITH PHENIX.REFINE.
Rfactor反射数%反射
Rfree0.2312 2694 5 %
Rwork0.1788 --
obs0.1815 53583 86.07 %
溶媒の処理減衰半径: 0.98 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 36.786 Å2 / ksol: 0.373 e/Å3
原子変位パラメータBiso mean: 28.423 Å2
Baniso -1Baniso -2Baniso -3
1-4.1785 Å21.8881 Å2-5.8677 Å2
2--2.4317 Å2-2.4985 Å2
3----6.6102 Å2
精密化ステップサイクル: LAST / 解像度: 1.798→43.167 Å
タンパク質核酸リガンド溶媒全体
原子数5592 0 64 356 6012
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.0065753
X-RAY DIFFRACTIONf_angle_d1.0517793
X-RAY DIFFRACTIONf_dihedral_angle_d16.692265
X-RAY DIFFRACTIONf_chiral_restr0.069940
X-RAY DIFFRACTIONf_plane_restr0.005987
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7985-1.83120.3332970.23421614X-RAY DIFFRACTION52
1.8312-1.86640.3258910.22192018X-RAY DIFFRACTION64
1.8664-1.90450.2721180.21692090X-RAY DIFFRACTION68
1.9045-1.94590.28811060.24012476X-RAY DIFFRACTION78
1.9459-1.99120.26621680.20642869X-RAY DIFFRACTION93
1.9912-2.0410.27571490.19182961X-RAY DIFFRACTION95
2.041-2.09620.26731260.20642579X-RAY DIFFRACTION83
2.0962-2.15790.27161640.18182912X-RAY DIFFRACTION94
2.1579-2.22750.23481630.17092958X-RAY DIFFRACTION95
2.2275-2.30710.28731600.18242589X-RAY DIFFRACTION83
2.3071-2.39950.23011400.17872981X-RAY DIFFRACTION95
2.3995-2.50870.25581450.17982986X-RAY DIFFRACTION96
2.5087-2.64090.26981620.19042920X-RAY DIFFRACTION95
2.6409-2.80630.22271350.19082845X-RAY DIFFRACTION90
2.8063-3.0230.23321600.19612909X-RAY DIFFRACTION94
3.023-3.32710.2631600.19482870X-RAY DIFFRACTION93
3.3271-3.80830.19451590.16962710X-RAY DIFFRACTION87
3.8083-4.7970.17281440.13312786X-RAY DIFFRACTION90
4.797-43.17960.1841470.1632816X-RAY DIFFRACTION90
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.4768-0.1359-2.6198.9871-2.86842.4852-0.12660.7134-0.477-0.744-0.07120.65290.4184-0.49250.14410.15050.0335-0.01390.258-0.07920.1948-2.3746-3.6176-0.7704
23.24620.89262.78570.99720.73252.63120.0041-0.10410.01030.1214-0.1134-0.0915-0.22490.4390.14230.2267-0.0626-0.00810.37880.01460.03095.25571.688217.5778
31.3216-2.35681.39375.8664-2.38141.4745-0.2658-0.2826-0.08430.70530.22840.15340.085-0.03960.04660.3552-0.1881-0.02430.51890.1130.099912.4153-3.376728.3509
41.1744-0.18290.86921.8793-0.47051.0688-0.0715-0.3842-0.13770.74660.05030.25560.0753-0.1574-0.04660.44-0.06550.09940.51070.15970.15237.8219-6.909626.0613
53.340.1932-1.4612.0382-0.49512.4461-0.0163-0.3175-0.1190.2838-0.07380.04340.18610.00870.06780.3033-0.10820.05740.36520.09760.10172.2623-5.860620.2901
63.6217-1.3645.01928.4497-3.07137.1324-0.0854-0.8001-0.21750.86230.14160.3193-0.1499-0.3107-0.04080.2449-0.02770.01840.32120.03790.1148-5.3544-5.258815.3339
74.00150.3034-1.53733.83081.46412.09010.00030.0131-0.6308-0.0739-0.00460.4790.1614-0.24170.05250.1428-0.04230.03310.13880.03110.1798-6.2266-9.68828.3096
81.7866-2.07942.49254.27180.32189.0872-0.0025-0.0436-0.3849-0.1056-0.11290.39640.1527-0.19350.11080.1336-0.01050.01780.06260.01060.15341.1704-11.98243.3677
97.16557.49767.88988.38778.2838.80270.1996-0.2371-0.04730.2194-0.1916-0.13330.2771-0.10250.00620.1834-0.0223-0.0430.27150.020.106611.9544-2.36313.2219
101.7329-0.81320.59811.38230.28421.30790.2752-0.5283-0.33290.0286-0.0494-0.1610.2964-0.1485-0.18330.2546-0.1178-0.06940.39280.12340.228415.1906-6.307120.1312
110.34991.3676-0.05197.3024-2.77063.3724-0.1915-0.4879-0.50050.0838-0.4087-0.66590.21430.86620.65520.3103-0.1274-0.02790.43540.21930.32435.422-14.420317.2997
121.33680.6442-0.99052.4530.49952.82860.0447-0.1861-0.71990.1415-0.0717-0.12870.431-0.07480.03870.1957-0.0117-0.01850.12350.09280.30255.7873-15.027210.1426
133.8166-0.0632-2.96221.9671-0.39882.40140.1463-0.18080.23910.10650.07210.0202-0.0537-0.1446-0.20890.24120.01860.01830.21250.01830.133816.94453.735912.3513
146.15574.2082-3.24443.7495-1.15912.99570.4482-0.59910.05850.7851-0.301-0.1585-0.40580.0449-0.06710.2125-0.05840.02090.2746-0.05450.088814.02669.660619.7776
154.33340.37064.28183.02833.36318.49710.0549-0.29710.16320.17550.0104-0.0485-0.090.3595-0.00170.1803-0.0045-0.01710.230.02830.08086.6135-0.796912.5322
163.79630.39950.12183.97660.17612.70560.07620.2670.0153-0.329-0.18620.4975-0.0419-0.25030.07090.12930.0185-0.01080.1830.00710.1306-5.8498-1.50061.3684
174.35370.47224.36864.7421.44634.7816-0.0978-0.4553-0.02280.0822-0.20970.2021-0.1713-0.20260.22490.1975-0.01310.040.2088-0.05340.0863-2.4042.683113.5895
184.70490.7521-4.24087.19120.46187.28170.04590.5290.0709-0.7468-0.07320.0551-0.2534-0.37020.05940.3414-0.08520.06230.425-0.14020.08981.1398.348918.8543
193.2684-2.9953.33243.5582-3.00993.4029-0.10310.0918-0.0223-0.03020.1016-0.2843-0.00690.12480.01160.14150.00350.00980.1613-0.06090.23136.2672-13.7005-1.769
204.39822.4682-0.49392.6208-0.37790.55740.0646-0.2166-0.28260.1797-0.2009-0.4899-0.05530.17210.05440.1682-0.0092-0.0950.14430.15160.543429.695-14.60347.5204
218.8399-0.6769-0.52263.21840.11053.10310.03360.2415-0.7836-0.1187-0.1657-0.02490.54240.34720.12040.16550.0642-0.03630.2258-0.02920.489535.4657-9.55112.4408
221.25870.2887-0.07522.78371.07391.68120.01760.0643-0.19970.00540.0723-0.31550.27890.2157-0.06550.21870.0745-0.02150.2165-0.16260.576829.2302-14.0525-1.234
235.79780.78082.44858.31353.26595.2549-0.07990.2344-0.4081-0.0910.0559-0.13290.15250.15920.03940.17670.04730.02440.223-0.10980.527520.6595-18.1218-3.8033
241.0984-0.20080.28833.5012-2.89782.41250.06280.1046-0.3054-0.21850.0848-0.31310.5044-0.0297-0.1830.2887-0.0191-0.04350.2569-0.26040.60614.8447-21.9392-6.3793
253.0151.62670.81581.3726-0.5212.25950.14330.386-0.4424-0.4429-0.0142-0.17420.20670.1097-0.13330.2871-0.08120.06570.2908-0.18930.21711.8686-11.7687-11.4423
263.5649-0.80571.26580.5549-1.182.58880.01480.2388-0.41440.0577-0.0454-0.17140.4260.03260.0540.16330.00840.03150.0746-0.0250.214217.5641-6.26120.8454
273.1793-0.339-2.77743.4320.45742.45550.1938-0.2353-0.35810.19370.1384-0.074-0.12460.2203-0.20980.13920.0158-0.04630.18850.00710.20229.2617-3.84317.3564
289.1051-0.2103-1.66648.22555.69346.0682-0.24030.88310.119-1.18110.2645-0.2875-0.7410.4831-0.01420.3157-0.0740.00470.2511-0.10890.29726.0289-6.2563-5.6315
295.7598-3.136-4.18193.37642.43323.96110.0364-0.02670.0407-0.1165-0.0284-0.18250.11680.3036-0.02470.3443-0.07890.14040.4477-0.15860.167721.7181-9.2167-12.6548
306.25512.1287.09211.47232.03278.5253-0.01430.106-0.14210.1630.0585-0.13270.0563-0.12710.02970.1991-0.0139-0.00740.1973-0.04390.164118.4055-3.0573-1.8193
310.01410.222-0.15565.3744-4.59124.18360.0872-0.2849-0.12470.3306-0.3149-0.3827-0.06140.48070.27590.3073-0.051-0.09560.26570.1640.249321.3001-5.581616.4896
325.0191-0.7090.31434.06270.15423.76080.0193-0.4343-0.40580.4887-0.1921-0.12350.1130.12340.08890.1796-0.0165-0.03090.17620.1260.464524.1723-11.505810.4546
333.42582.59270.84944.26390.94162.0971-0.16610.1347-0.3535-0.29570.1622-0.08480.101-0.10260.00890.1086-0.01690.00810.148-0.08940.30246.8478-15.1831-3.3017
342.14422.63360.53283.68840.09421.3756-0.10110.2085-0.3723-0.19720.0778-0.03390.2638-0.0444-0.00470.1851-0.0394-0.01640.0955-0.09730.6169.7448-22.13921.3986
351.05640.46950.86952.1211-0.3771.7105-0.1151-0.0830.10650.10150.0027-0.0743-0.03180.05020.03630.180.0544-0.12980.16630.1070.606723.8021-19.76527.9026
365.7431.5617-3.70310.5411-0.46354.9231-0.23820.4088-0.633-0.11260.08010.90010.7095-0.69450.14530.8179-0.275-0.13410.46880.1371.243918.1558-21.50811.8552
372.72660.9084-2.19996.1893-1.78112.5829-0.14030.3323-0.1085-0.3106-0.13730.35740.1448-0.33670.23870.1764-0.029-0.01810.3855-0.06520.12147.543-2.6799-8.9753
382.91933.16623.32834.86214.67724.5953-0.22420.12890.3815-0.46050.05-0.1087-0.6477-0.04590.20060.2252-0.0256-0.02920.15930.07690.189822.507415.6545-0.1014
393.7480.86431.9754.89141.38232.675-0.1756-0.0720.84360.11480.12670.1359-0.6743-0.16550.02070.26970.0599-0.01860.09760.01950.252117.488219.67895.8266
403.8812-2.54431.05893.00550.5762.9917-0.2970.37530.8828-0.40280.08730.1133-0.88170.0560.12620.23690.0038-0.0530.19210.0890.230214.367917.0921-2.6986
413.3495-2.54010.5333.41192.57537.14050.03340.27620.2984-0.52110.0414-0.1344-0.5576-0.0016-0.09320.2316-0.0234-0.00590.27410.1740.197910.034212.6477-8.1635
421.2984-0.43830.50412.7443-1.79246.4690.03680.32050.2121-0.305-0.0899-0.1151-0.2810.20270.07450.2526-0.0882-0.0360.44910.22730.17117.50559.3235-13.689
435.99383.4686-1.76368.56614.12264.55240.15480.43280.1768-0.64410.02280.5133-0.0404-0.4163-0.14090.21580.0201-0.04030.33890.03720.1344-0.85095.7948-6.758
445.48315.30473.74555.13393.62072.5693-0.27190.20470.2855-0.1970.09870.2453-0.09030.17720.1790.13760.020.00350.12310.04450.084213.41244.40953.0808
458.6944-0.0052-0.7091.81530.39973.52570.0174-0.44020.19370.31510.02560.0966-0.1129-0.057-0.02560.21170.0021-0.00780.1186-0.00430.135816.514412.93018.984
465.5533-1.09562.13186.04414.68395.742-0.2383-0.49310.63990.63960.19590.7296-0.846-0.52640.03730.27580.0236-0.02230.15990.04130.40675.368815.26961.891
471.77211.5282-0.9722.10930.7213.5954-0.04550.11280.4252-0.0050.02240.2876-0.12070.02440.01170.14390.0125-0.01380.08470.01180.13933.75988.10712.5491
489.908-1.5281-3.46930.23670.53411.217-0.0133-0.17670.1284-0.0067-0.0423-0.17680.10160.26730.05270.2010.01250.00540.17260.04580.167226.47682.1216.3104
495.3537-0.511-0.59771.4907-0.45531.2195-0.128-0.1003-0.07660.17390.0644-0.22330.05140.06190.05050.14440.0017-0.0090.12990.04590.108423.68728.40620.9165
504.9583-2.46722.90976.61821.08734.8329-0.10680.3523-0.1737-0.44880.07320.42770.3345-0.47730.06420.1533-0.0536-0.00740.2680.01210.08036.34370.6356-6.6164
511.1999-1.11292.5612.2642-0.21989.23670.29020.3602-0.2033-0.4086-0.32820.24080.3877-0.36670.07660.4175-0.09570.0330.5363-0.1590.20759.1218-3.1296-16.7311
523.00642.93273.64456.56194.36274.6791-0.2270.44450.1101-0.9663-0.04520.1134-0.39910.15940.17060.2619-0.0081-0.00660.46760.02780.08913.71383.9775-14.3139
535.62560.19991.25651.8697-0.03484.2842-0.16070.16850.0210.15080.0071-0.0807-0.1048-0.02290.10910.1821-0.00910.0240.23070.10480.13922.915612.0194-6.9603
545.671-3.3942-4.07272.73570.98326.26270.02671.2838-0.7642-1.4022-0.12490.72810.5653-0.34430.07890.3780.0087-0.03830.3774-0.02930.296125.27856.2751-10.2081
554.9443-1.0996-4.21277.16471.53688.81470.0846-0.18460.54830.0293-0.1265-0.219-0.40030.22210.08820.10770.02410.00790.1052-0.00850.191744.565319.950439.9964
564.09823.0591-0.89344.02741.10263.8312-0.05890.5123-0.6854-0.36110.1573-0.1350.40960.0137-0.08540.22980.0473-0.0410.2409-0.15410.302534.30461.101725.663
570.64561.210.37762.28190.50713.1522-0.09620.115-0.2934-0.06690.0496-0.15110.5540.09810.02280.28210.0733-0.1120.1631-0.18780.452133.0299-4.189631.5557
582.26970.2133-0.26193.1331.01555.3624-0.07550.1712-0.347-0.00190.0334-0.07890.58740.14130.10530.26810.1018-0.05720.1968-0.21670.359640.2571-0.77232.387
595.47731.90370.69544.80641.7036.75590.08150.0811-0.6297-0.1797-0.0766-0.11560.40270.21220.070.16670.0669-0.02390.0994-0.03390.152845.34615.44835.4839
609.36240.78540.16746.4598-5.69245.09620.02810.1379-0.4377-0.38530.0334-0.34810.49480.4673-0.06470.11450.04940.00880.1855-0.05350.227951.09559.566437.5921
612.1613-0.1062-0.76015.68590.70954.65210.0137-0.5636-0.37140.55750.0182-0.68260.23750.5803-0.03790.11770.0489-0.02320.17870.03950.147845.886910.875947.9226
625.45323.24721.52696.16452.38623.3110.0060.2185-0.1338-0.24020.02570.02190.08880.07770.08270.11110.05820.02880.0646-0.05390.101135.210712.329940.2155
631.03561.192-0.64922.7559-0.21970.60920.09320.3718-0.3125-0.18580.09280.19320.1503-0.2489-0.21130.1640.0323-0.06050.2177-0.0710.241226.35383.426430.4989
644.11421.51632.19316.80540.47131.71970.0708-1.0414-0.55880.7833-0.0982-0.09830.3696-0.54080.08450.247-0.0006-0.05090.2449-0.00250.326234.26270.940140.9773
655.5377-2.7549-2.37073.7625-0.55822.37550.0201-0.1254-0.67190.1128-0.01890.01710.5270.0960.08490.25770.0284-0.07660.07310.04770.219240.13333.501446.8546
668.9201-3.34587.07964.8004-3.18855.6996-0.0850.2298-0.0288-0.1917-0.10770.0714-0.1388-0.04350.18320.1221-0.0274-0.00640.1793-0.03850.13328.591510.902735.7028
676.6157-3.30175.37514.7092-3.65884.67870.1760.3354-0.1488-0.04170.25160.19530.1989-0.2309-0.38850.2447-0.0249-0.00490.3510.00750.136927.580313.587321.1593
685.49284.35723.99217.94725.37053.9810.03520.4803-0.0564-0.1949-0.12880.28030.0081-0.16360.08250.20110.0217-0.00440.2022-0.07310.159433.82398.945528.3942
694.2746-0.28191.12592.2224-0.27673.09380.04450.02750.26690.0869-0.0246-0.1562-0.0650.3746-0.03750.10220.0170.03280.121-0.00380.136147.747819.627640.0703
705.57864.42263.37273.63062.46272.4112-0.01370.3438-0.2833-0.28080.2142-0.77740.16880.5825-0.10640.11810.03630.04180.2288-0.05250.219848.949915.715332.173
715.0804-0.22741.91760.5102-1.37835.7711-0.13140.1128-0.1928-0.1946-0.03450.1704-0.0105-0.10050.13430.23720.05180.01140.3087-0.1260.173441.34726.775423.9952
723.9471-1.7354-0.21481.9386-0.32790.3166-0.115-0.24040.4850.06010.2431-0.3772-0.67460.5511-0.11850.44760.09270.05190.4922-0.06740.222243.32513.21821.6211
737.67523.4776-1.29172.9624-1.4740.7891-0.09270.0487-0.09230.03530.2071-0.1146-0.129-0.0643-0.0660.1286-0.00230.01150.1734-0.00050.107335.250516.104250.7311
742.8835-0.8612.96651.36310.06693.87160.4017-0.9324-0.89060.1773-0.09020.3970.4467-0.4721-0.14930.1578-0.0709-0.03140.30890.12790.271511.22627.982646.9474
755.01550.60072.81997.56663.03357.1677-0.0551-0.5247-0.18120.64770.05550.55380.0028-0.3153-0.04950.1194-0.00890.05540.2681-0.00410.14828.991615.898545.7721
761.6381.44761.27924.7092-0.41831.69820.1559-0.4750.19740.6388-0.07920.90960.2109-0.6833-0.03420.18020.0210.07870.4090.03730.188914.433815.744352.6448
774.3381.62612.28555.68211.4384.6483-0.0848-0.26670.00120.34260.05510.189-0.2297-0.12720.01390.15560.00420.03630.3287-0.03610.087922.546716.533355.955
783.8125-3.9169-2.37344.21971.41426.8365-0.1017-1.0098-0.15321.14350.13160.42790.4307-0.1358-0.04140.2447-0.03570.05540.4190.00270.122828.409317.058760.5365
791.7658-0.5438-0.20643.87960.73584.54690.0254-0.280.2020.3150.06110.0482-0.25060.0067-0.07350.17790.04160.05190.2353-0.19840.238231.398225.87452.5626
805.39596.91926.23069.4547.31167.99330.1036-0.12240.12230.07770.0311-0.0552-0.02650.1254-0.0830.1460.01980.03340.1167-0.01920.126620.954814.002440.7039
813.37562.88892.95814.10761.10663.83150.0119-0.0960.23770.0183-0.06950.1489-0.22-0.02280.0330.14530.02580.01380.1994-0.02880.169414.805119.438242.0401
822.0843-1.8436-0.36513.62162.02962.64290.14160.07980.0205-0.2621-0.15730.0332-0.1599-0.18870.04150.23860.06260.10870.3036-0.25630.329919.859826.869452.6579
834.2091-0.23370.18763.5481-1.68030.79690.019-0.32230.3826-0.14770.0182-0.0931-0.5996-0.1411-0.03150.21550.05210.11770.1535-0.07710.28124.989528.532846.6112
844.4013-4.5266-3.60844.70133.79573.112-0.0144-0.06010.0997-0.18360.0144-0.1799-0.01870.0098-0.15690.24250.0021-0.01090.11010.02370.149123.071912.624336.4308
853.2935-3.481-4.11983.67754.35335.15210.0380.232-0.6271-0.099-0.17390.38480.5231-0.32690.15340.2975-0.0094-0.08460.1419-0.04060.300118.35122.126438.3192
865.69222.67891.36872.5849-0.21471.85930.1049-0.22780.0295-0.04010.05180.02260.1150.0146-0.12820.11840.00220.00250.13630.00190.151426.481314.61646.7555
871.8279-1.76190.4022.0993-0.62193.5682-0.0807-0.43440.35070.44140.1305-0.4276-0.24060.31710.03140.156-0.0027-0.01930.2655-0.0530.185639.718917.078956.0038
883.6733-1.68261.31575.7678-1.35013.246-0.0529-0.26660.02260.581-0.0042-0.05420.158-0.07380.02850.2387-0.0295-0.02260.37340.05710.062134.614310.174757.2555
891.5520.36893.07953.71130.1357.7890.03580.02250.0209-0.05820.05270.12820.1489-0.1146-0.05790.1466-0.04590.02330.24850.13510.13120.15856.245751.9811
905.9904-2.8978-1.82523.93531.95853.8406-0.0773-0.572-0.00860.8633-0.1425-1.09360.13390.97340.26960.32340.0049-0.07140.35820.18220.349625.11111.353951.4406
911.6296-1.469-0.40588.8788-0.54718.7687-0.2382-0.34490.50010.63790.0704-0.6085-0.17290.61090.15440.2157-0.03080.00840.1708-0.09920.324937.416128.595946.6016
921.1551.54950.4042.73310.84860.28480.1901-0.1135-0.0051-0.02530.0591-0.0310.2132-0.2914-0.20740.2180.0391-0.02190.17090.06130.37623.455829.766931.1325
934.0949-2.96851.02824.6351.97193.53120.03321.02310.7306-0.8164-0.15580.2375-0.7012-0.56880.06250.3980.0155-0.09640.44350.13380.242822.907127.334517.3514
941.60161.77760.22673.47622.50854.1969-0.00590.20880.4381-0.47120.10780.142-0.6364-0.0678-0.10680.2479-0.0311-0.00540.20620.19690.414528.884231.377622.904
958.8072.09212.20557.52931.44185.0401-0.05270.22670.3948-0.25060.0522-0.1814-0.56120.0935-0.07750.2584-0.04470.03420.13450.11590.396432.611635.168931.1416
965.56624.942-2.91447.6208-0.88598.7978-0.1398-0.00080.7889-0.29160.01130.7259-0.8231-0.10530.07290.2897-0.0598-0.03770.1420.00690.581435.641638.929836.6672
972.9663-1.4609-0.84785.5273-3.99534.2926-0.0118-0.07710.56970.1965-0.0419-0.4861-0.63850.53820.03140.133-0.06180.020.15530.010.320444.024130.975836.711
981.70921.3041.30621.3120.60515.5638-0.02590.18490.2268-0.0624-0.0020.0674-0.251-0.0729-0.01780.13770.00570.01240.0180.06030.159828.475121.633731.935
992.45811.71012.18623.3351.47393.3343-0.05940.5415-0.0347-0.19380.2284-0.10430.02370.4306-0.13830.24690.0132-0.00040.32420.04020.132129.56521.792522.7721
1004.26790.7961-2.28180.96870.67574.8952-0.31920.8894-0.0112-0.46520.4690.06710.0702-0.4772-0.1190.2048-0.08020.05960.48080.21360.369940.581529.35925.8074
1015.8252-2.88532.61193.76991.19253.8111-0.21810.33430.1042-0.28030.0654-0.3034-0.06230.34040.12630.12670.01190.02870.14690.04250.108840.228722.126230.0694
1024.8851-1.107-5.69674.6175-0.29877.4910.1726-0.37960.15030.58580.0260.08330.0821-0.0661-0.1390.2628-0.012-0.00360.1874-0.02990.100620.626217.283833.1371
1031.97213.6693-3.0976.8494-5.77754.8724-0.190.59180.5743-0.22820.51330.78830.1494-0.6628-0.3250.1782-0.0001-0.02250.3050.04240.309613.213423.441530.4993
1044.72040.44434.70650.82460.35194.706-0.007-0.10710.43630.0167-0.00850.1511-0.1997-0.12420.01890.15140.00350.01420.1282-0.00390.232329.283426.538435.4738
1053.3392-1.2313-3.85575.25952.20255.5527-0.0908-0.55610.44660.21570.3889-0.4764-0.15150.7075-0.36510.3210.0246-0.01120.3301-0.20780.392437.483433.583347.2876
1062.19560.5608-0.57994.50971.77183.4775-0.0615-0.06550.36770.22290.07820.0742-0.67720.0171-0.04540.36980.04750.01050.075-0.09410.476629.958237.008544.3978
1074.03542.7728-0.63085.841.28390.8480.02140.11910.0629-0.13420.09920.39740.0596-0.1186-0.12290.17020.0376-0.04080.14230.12090.521121.315534.403131.5904
1082.2446-0.0944-2.88622.0148-1.09537.3292-0.0188-0.27670.37771.11980.1367-1.0013-0.67350.3637-0.12330.62080.0818-0.05680.2026-0.05630.716217.868334.653937.6045
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:6)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 7:12)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 13:17)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 18:22)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 23:28)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 29:34)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 35:39)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 40:44)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 45:51)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 52:60)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 61:65)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 66:75)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 76:80)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 81:87)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 88:93)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 94:104)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 105:109)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 110:117)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 1:7)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 8:14)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 15:19)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 20:26)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 27:32)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 33:37)
25X-RAY DIFFRACTION25(CHAIN B AND RESID 38:43)
26X-RAY DIFFRACTION26(CHAIN B AND RESID 44:49)
27X-RAY DIFFRACTION27(CHAIN B AND RESID 50:57)
28X-RAY DIFFRACTION28(CHAIN B AND RESID 58:63)
29X-RAY DIFFRACTION29(CHAIN B AND RESID 64:70)
30X-RAY DIFFRACTION30(CHAIN B AND RESID 71:76)
31X-RAY DIFFRACTION31(CHAIN B AND RESID 77:83)
32X-RAY DIFFRACTION32(CHAIN B AND RESID 84:91)
33X-RAY DIFFRACTION33(CHAIN B AND RESID 92:101)
34X-RAY DIFFRACTION34(CHAIN B AND RESID 102:107)
35X-RAY DIFFRACTION35(CHAIN B AND RESID 108:112)
36X-RAY DIFFRACTION36(CHAIN B AND RESID 113:117)
37X-RAY DIFFRACTION37(CHAIN C AND RESID 1:7)
38X-RAY DIFFRACTION38(CHAIN C AND RESID 8:14)
39X-RAY DIFFRACTION39(CHAIN C AND RESID 15:21)
40X-RAY DIFFRACTION40(CHAIN C AND RESID 22:27)
41X-RAY DIFFRACTION41(CHAIN C AND RESID 28:32)
42X-RAY DIFFRACTION42(CHAIN C AND RESID 33:37)
43X-RAY DIFFRACTION43(CHAIN C AND RESID 38:42)
44X-RAY DIFFRACTION44(CHAIN C AND RESID 43:51)
45X-RAY DIFFRACTION45(CHAIN C AND RESID 52:60)
46X-RAY DIFFRACTION46(CHAIN C AND RESID 61:65)
47X-RAY DIFFRACTION47(CHAIN C AND RESID 66:76)
48X-RAY DIFFRACTION48(CHAIN C AND RESID 77:82)
49X-RAY DIFFRACTION49(CHAIN C AND RESID 83:91)
50X-RAY DIFFRACTION50(CHAIN C AND RESID 92:97)
51X-RAY DIFFRACTION51(CHAIN C AND RESID 98:102)
52X-RAY DIFFRACTION52(CHAIN C AND RESID 103:107)
53X-RAY DIFFRACTION53(CHAIN C AND RESID 108:112)
54X-RAY DIFFRACTION54(CHAIN C AND RESID 113:117)
55X-RAY DIFFRACTION55(CHAIN D AND RESID 1:7)
56X-RAY DIFFRACTION56(CHAIN D AND RESID 8:15)
57X-RAY DIFFRACTION57(CHAIN D AND RESID 16:21)
58X-RAY DIFFRACTION58(CHAIN D AND RESID 22:26)
59X-RAY DIFFRACTION59(CHAIN D AND RESID 27:32)
60X-RAY DIFFRACTION60(CHAIN D AND RESID 33:37)
61X-RAY DIFFRACTION61(CHAIN D AND RESID 38:42)
62X-RAY DIFFRACTION62(CHAIN D AND RESID 43:48)
63X-RAY DIFFRACTION63(CHAIN D AND RESID 49:57)
64X-RAY DIFFRACTION64(CHAIN D AND RESID 58:63)
65X-RAY DIFFRACTION65(CHAIN D AND RESID 64:72)
66X-RAY DIFFRACTION66(CHAIN D AND RESID 73:78)
67X-RAY DIFFRACTION67(CHAIN D AND RESID 79:85)
68X-RAY DIFFRACTION68(CHAIN D AND RESID 86:92)
69X-RAY DIFFRACTION69(CHAIN D AND RESID 93:102)
70X-RAY DIFFRACTION70(CHAIN D AND RESID 103:107)
71X-RAY DIFFRACTION71(CHAIN D AND RESID 108:112)
72X-RAY DIFFRACTION72(CHAIN D AND RESID 113:117)
73X-RAY DIFFRACTION73(CHAIN E AND RESID 1:9)
74X-RAY DIFFRACTION74(CHAIN E AND RESID 10:14)
75X-RAY DIFFRACTION75(CHAIN E AND RESID 15:21)
76X-RAY DIFFRACTION76(CHAIN E AND RESID 22:26)
77X-RAY DIFFRACTION77(CHAIN E AND RESID 27:32)
78X-RAY DIFFRACTION78(CHAIN E AND RESID 33:37)
79X-RAY DIFFRACTION79(CHAIN E AND RESID 38:44)
80X-RAY DIFFRACTION80(CHAIN E AND RESID 45:52)
81X-RAY DIFFRACTION81(CHAIN E AND RESID 53:62)
82X-RAY DIFFRACTION82(CHAIN E AND RESID 63:68)
83X-RAY DIFFRACTION83(CHAIN E AND RESID 69:74)
84X-RAY DIFFRACTION84(CHAIN E AND RESID 75:79)
85X-RAY DIFFRACTION85(CHAIN E AND RESID 80:87)
86X-RAY DIFFRACTION86(CHAIN E AND RESID 88:95)
87X-RAY DIFFRACTION87(CHAIN E AND RESID 96:101)
88X-RAY DIFFRACTION88(CHAIN E AND RESID 102:106)
89X-RAY DIFFRACTION89(CHAIN E AND RESID 107:112)
90X-RAY DIFFRACTION90(CHAIN E AND RESID 113:117)
91X-RAY DIFFRACTION91(CHAIN F AND RESID 1:6)
92X-RAY DIFFRACTION92(CHAIN F AND RESID 7:12)
93X-RAY DIFFRACTION93(CHAIN F AND RESID 13:19)
94X-RAY DIFFRACTION94(CHAIN F AND RESID 20:26)
95X-RAY DIFFRACTION95(CHAIN F AND RESID 27:32)
96X-RAY DIFFRACTION96(CHAIN F AND RESID 33:37)
97X-RAY DIFFRACTION97(CHAIN F AND RESID 38:42)
98X-RAY DIFFRACTION98(CHAIN F AND RESID 43:52)
99X-RAY DIFFRACTION99(CHAIN F AND RESID 53:62)
100X-RAY DIFFRACTION100(CHAIN F AND RESID 63:68)
101X-RAY DIFFRACTION101(CHAIN F AND RESID 69:75)
102X-RAY DIFFRACTION102(CHAIN F AND RESID 76:80)
103X-RAY DIFFRACTION103(CHAIN F AND RESID 81:87)
104X-RAY DIFFRACTION104(CHAIN F AND RESID 88:95)
105X-RAY DIFFRACTION105(CHAIN F AND RESID 96:101)
106X-RAY DIFFRACTION106(CHAIN F AND RESID 102:106)
107X-RAY DIFFRACTION107(CHAIN F AND RESID 107:112)
108X-RAY DIFFRACTION108(CHAIN F AND RESID 113:117)

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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