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- PDB-4m8d: Crystal structure of an isatin hydrolase bound to product analogu... -

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基本情報

登録情報
データベース: PDB / ID: 4m8d
タイトルCrystal structure of an isatin hydrolase bound to product analogue thioisatinate
要素Putative uncharacterized protein
キーワードHYDROLASE / Isatin hydrolysis / Thioisatinate (product analogue)
機能・相同性
機能・相同性情報


isatin hydrolase / arylformamidase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / tryptophan catabolic process to kynurenine / manganese ion binding
類似検索 - 分子機能
Putative cyclase / Kynurenine formamidase/cyclase-like / Kynurenine formamidase superfamily / Putative cyclase / Glucose Oxidase; domain 1 / 3-Layer(bba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
oxo(2-sulfanylphenyl)acetic acid / : / Isatin hydrolase
類似検索 - 構成要素
生物種Labrenzia aggregata (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: 1.9 Å
データ登録者Bjerregaard-Andersen, K. / Sommer, T. / Jensen, J.K. / Jochimsen, B. / Etzerodt, M. / Morth, J.P.
引用ジャーナル: J.Biol.Chem. / : 2014
タイトル: A proton wire and water channel revealed in the crystal structure of isatin hydrolase.
著者: Bjerregaard-Andersen, K. / Sommer, T. / Jensen, J.K. / Jochimsen, B. / Etzerodt, M. / Morth, J.P.
履歴
登録2013年8月13日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年6月18日Provider: repository / タイプ: Initial release
改定 1.12014年7月16日Group: Database references
改定 1.22014年8月20日Group: Database references
改定 1.32018年3月7日Group: Data collection / カテゴリ: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
改定 1.42023年9月20日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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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: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
E: Putative uncharacterized protein
F: Putative uncharacterized protein
G: Putative uncharacterized protein
H: Putative uncharacterized protein
I: Putative uncharacterized protein
J: Putative uncharacterized protein
K: Putative uncharacterized protein
L: Putative uncharacterized protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)340,46752
ポリマ-336,98012
非ポリマー3,48740
59,9723329
1
A: Putative uncharacterized protein
B: Putative uncharacterized protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,87812
ポリマ-56,1632
非ポリマー71510
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-101 kcal/mol
Surface area18660 Å2
手法PISA
2
C: Putative uncharacterized protein
D: Putative uncharacterized protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,7589
ポリマ-56,1632
非ポリマー5957
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-95 kcal/mol
Surface area18590 Å2
手法PISA
3
E: Putative uncharacterized protein
F: Putative uncharacterized protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,6787
ポリマ-56,1632
非ポリマー5145
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area8890 Å2
ΔGint-79 kcal/mol
Surface area18540 Å2
手法PISA
4
G: Putative uncharacterized protein
H: Putative uncharacterized protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,6386
ポリマ-56,1632
非ポリマー4744
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-81 kcal/mol
Surface area18390 Å2
手法PISA
5
I: Putative uncharacterized protein
J: Putative uncharacterized protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,7589
ポリマ-56,1632
非ポリマー5957
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-89 kcal/mol
Surface area18280 Å2
手法PISA
6
K: Putative uncharacterized protein
L: Putative uncharacterized protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,7589
ポリマ-56,1632
非ポリマー5957
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area8900 Å2
ΔGint-85 kcal/mol
Surface area18440 Å2
手法PISA
単位格子
Length a, b, c (Å)84.980, 51.820, 357.090
Angle α, β, γ (deg.)90.00, 91.92, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Putative uncharacterized protein


分子量: 28081.643 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Labrenzia aggregata (バクテリア)
: IAM 12614 / 遺伝子: SIAM614_09648 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0NLY7
#2: 化合物
ChemComp-MN / MANGANESE (II) ION


分子量: 54.938 Da / 分子数: 12 / 由来タイプ: 合成 / : Mn
#3: 化合物
ChemComp-23J / oxo(2-sulfanylphenyl)acetic acid / 2-(2-メルカプトフェニル)グリオキシル酸


分子量: 182.196 Da / 分子数: 12 / 由来タイプ: 合成 / : C8H6O3S
#4: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 16 / 由来タイプ: 合成 / : Ca
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 3329 / 由来タイプ: 天然 / : 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: 2.33 Å3/Da / 溶媒含有率: 47.25 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5
詳細: 16% w/V PEG3350, 0.2 M calcium acetate, 1 mM MnCl2, 1 mM thioisatin (Benzo[b]thiophene-2,3-dione), pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: PETRA III, EMBL c/o DESY / ビームライン: P13 (MX1) / 波長: 1.2395 Å
検出器タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2013年4月30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: 1.2395 Å / 相対比: 1
反射解像度: 1.9→49.506 Å / Num. obs: 471486 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / 冗長度: 3.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.53
反射 シェル解像度: 1.9→2 Å / 冗長度: 3.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.83 / % possible all: 96.5

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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
PHENIX(phenix.phaser: 1.8.1_1168)モデル構築
PHENIX(phenix.refine: 1.8.1_1168)精密化
XDSデータ削減
XSCALEデータスケーリング
PHENIX1.8.1_1168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 4J0N
解像度: 1.9→29.976 Å / SU ML: 0.17 / σ(F): 1.99 / 位相誤差: 18.72 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.1923 23591 5.01 %
Rwork0.152 --
obs0.154 471287 98.21 %
all-291160 -
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 1.9→29.976 Å
タンパク質核酸リガンド溶媒全体
原子数23679 0 172 3329 27180
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.0124675
X-RAY DIFFRACTIONf_angle_d1.06233462
X-RAY DIFFRACTIONf_dihedral_angle_d12.6798811
X-RAY DIFFRACTIONf_chiral_restr0.0463642
X-RAY DIFFRACTIONf_plane_restr0.0064424
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.26567910.22814976X-RAY DIFFRACTION97
1.9216-1.94420.25777800.214414782X-RAY DIFFRACTION98
1.9442-1.96790.26117880.208314875X-RAY DIFFRACTION98
1.9679-1.99280.2337890.197615060X-RAY DIFFRACTION98
1.9928-2.0190.24147720.193114728X-RAY DIFFRACTION98
2.019-2.04670.22497730.18114745X-RAY DIFFRACTION98
2.0467-2.07590.22417960.179215145X-RAY DIFFRACTION98
2.0759-2.10690.22387710.182614620X-RAY DIFFRACTION98
2.1069-2.13980.237880.18114868X-RAY DIFFRACTION98
2.1398-2.17490.2147850.166514935X-RAY DIFFRACTION98
2.1749-2.21240.22887780.174514758X-RAY DIFFRACTION98
2.2124-2.25260.2257870.161214949X-RAY DIFFRACTION97
2.2526-2.29590.20687710.156414671X-RAY DIFFRACTION98
2.2959-2.34270.20367900.150614858X-RAY DIFFRACTION98
2.3427-2.39360.20647780.153714875X-RAY DIFFRACTION98
2.3936-2.44930.20587910.154715032X-RAY DIFFRACTION99
2.4493-2.51050.19787940.153514974X-RAY DIFFRACTION99
2.5105-2.57840.21318000.154415212X-RAY DIFFRACTION99
2.5784-2.65420.20787840.156114846X-RAY DIFFRACTION99
2.6542-2.73980.22028010.157615170X-RAY DIFFRACTION99
2.7398-2.83770.21447840.154114853X-RAY DIFFRACTION98
2.8377-2.95120.19787910.15314890X-RAY DIFFRACTION98
2.9512-3.08540.20627740.156414904X-RAY DIFFRACTION98
3.0854-3.24790.20017970.149914990X-RAY DIFFRACTION98
3.2479-3.45110.17717920.148715023X-RAY DIFFRACTION99
3.4511-3.71710.16627960.137415084X-RAY DIFFRACTION99
3.7171-4.09030.15917870.12914977X-RAY DIFFRACTION99
4.0903-4.68030.13047980.106215120X-RAY DIFFRACTION99
4.6803-5.88930.14247840.12114934X-RAY DIFFRACTION98
5.8893-29.97970.16877810.146914842X-RAY DIFFRACTION98
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)
11.49910.07480.1760.6313-0.25010.9270.01630.032-0.0897-0.0464-0.06390.14470.0402-0.1448-0.01080.1483-0.0320.01490.10110.00220.147616.70325.179391.5542
21.06830.1698-0.23710.9495-0.10071.1686-0.01450.03010.1741-0.08910.03540.0563-0.1374-0.0468-0.01550.1683-0.01670.02220.0601-0.00810.164820.957916.234291.8547
30.63460.27780.77761.67410.22491.0959-0.1207-0.3538-0.21030.0584-0.08420.25460.2696-0.3573-0.61330.2447-0.08380.12950.12380.05920.20589.6825-1.92111.7995
41.4193-0.3068-0.64111.05070.15271.68770.0167-0.1585-0.05880.0501-0.04790.11280.0193-0.17960.01670.1341-0.03190.03970.1154-0.02120.137912.95276.5816106.7263
51.5706-0.0044-1.81150.1908-0.01132.1296-0.0882-0.87020.46770.18-0.19380.1288-0.0194-0.0619-0.30160.1751-0.02580.02990.301-0.13940.235619.747212.9861113.5695
60.349-0.4688-0.15550.7463-0.03650.8768-0.028-0.0425-0.0644-0.0042-0.0360.07390.0607-0.0614-0.04440.1429-0.03060.01690.0542-0.0140.147519.58474.852895.0843
71.26360.1748-0.14130.18890.34570.9976-0.04350.162-0.0298-0.13670.09730.1513-0.01650.0928-0.14680.188-0.0360.00560.1054-0.02390.167728.08887.840784.7848
81.1193-0.16460.27251.0759-0.51020.2758-0.0643-0.21070.4479-0.03820.0925-0.0223-0.6858-0.06830.28420.3001-0.03150.00570.0634-0.04880.286723.934626.968397.9169
91.32130.0883-0.18640.71010.28761.123-0.07610.2510.0977-0.0660.04180.1161-0.1162-0.12870.02280.1485-0.0268-0.00340.13160.01620.135818.696711.300378.6502
101.71750.3873-0.0541.864-0.97991.7357-0.02210.4893-0.1188-0.21490.0216-0.03960.19750.27080.03850.1945-0.05070.04670.3412-0.0570.145938.41493.957464.8942
111.2645-0.3762-0.1290.8177-0.69741.185-0.00690.3709-0.184-0.03120.0311-0.09280.15020.23620.06620.1434-0.0490.02670.2083-0.05030.126733.57975.069373.4353
120.8457-0.5733-0.18340.6869-0.17810.99610.08770.26860.251-0.0997-0.0718-0.1016-0.24130.23180.00610.254-0.10320.03260.27150.0320.178636.047521.623869.0912
131.42930.3727-0.470.7499-0.59191.1656-0.1010.4695-0.07-0.1820.12050.03650.00920.0114-0.00910.2105-0.06170.00730.2717-0.0220.136527.05476.606266.7488
140.2254-0.4285-0.35741.8022-0.44221.9575-0.19930.87220.4932-0.2491-0.0270.1155-0.07660.19690.14010.2223-0.094-0.05480.40780.09410.211922.335712.706162.3931
151.70540.3308-0.24081.03660.35171.7208-0.06440.1747-0.0881-0.01480.0661-0.01430.03950.0638-0.01080.1353-0.04310.01630.0735-0.01340.103626.24585.752781.1931
162.74411.1645-0.55933.7819-1.22291.9990.2229-0.0792-0.57670.0668-0.02380.11790.22160.093-0.04970.59350.0141-0.03590.14210.01880.271653.828512.327996.4799
171.03120.0595-0.41310.80910.17781.1956-0.13280.25490.1283-0.15970.1909-0.1099-0.11050.1934-0.03940.2907-0.1353-0.03350.22320.02550.210363.46235.476582.2264
181.3199-0.2779-0.77340.7831-0.45421.0101-0.0720.24770.0069-0.09610.072-0.19440.05040.27560.07550.3289-0.1830.01820.3955-0.00980.21671.598231.18874.5347
191.00830.3213-0.0930.2628-0.08430.0383-0.2690.6384-0.0451-0.38820.2602-0.02320.07540.07970.04130.3632-0.2843-0.01610.42260.00730.204161.912228.077569.7286
200.025-0.17610.04171.2044-0.27330.0873-0.11690.36270.1891-0.3144-0.2279-0.3759-0.0740.3602-0.52190.4629-0.4108-0.00790.71350.34460.176760.335.491265.1815
210.46990.14440.09620.90790.19081.7371-0.21950.3716-0.0325-0.10780.2114-0.00120.09890.3499-0.04070.2248-0.1483-0.00810.14870.01470.18460.500428.38383.8425
221.22140.022-0.22040.809-0.04111.1318-0.12740.1260.1994-0.11510.1527-0.0406-0.09170.0873-0.05150.233-0.084-0.05380.11310.02150.187256.812536.859194.3048
230.88150.0979-0.06891.00940.41521.4295-0.0418-0.09740.06270.14970.0321-0.00080.1070.00160.0160.2354-0.0249-0.05350.07970.00220.169949.573232.7782107.5966
242.58751.46511.04613.9121-2.36454.3955-0.0711-0.16470.00640.27020.28810.8726-0.075-0.4003-0.25390.25080.131-0.00380.43130.03960.3976-20.723437.7485141.8629
250.9567-0.1104-0.00681.42210.06961.43920.03140.00430.0704-0.01220.0054-0.2034-0.07260.3245-0.00730.11020.00790.00110.2515-0.00980.193412.256334.8576147.6286
261.04030.41090.2611.12670.29161.57470.0075-0.26680.14260.1983-0.05330.0644-0.0914-0.0787-0.03120.13840.02470.00270.2345-0.04510.1456-1.672438.418165.4939
270.8290.15750.19951.5530.03591.3059-0.0112-0.16230.0820.2289-0.0339-0.0476-0.0819-0.11440.0030.10720.0299-0.00680.1564-0.01280.1352-2.070934.7444159.6699
280.81390.18850.54791.0988-0.22141.07430.10710.12560.0164-0.1031-0.14540.01210.1165-0.2125-0.11240.15090.0466-0.01250.217-0.00310.1457-5.056727.523143.4905
291.28280.161-0.07450.98140.13940.03260.0602-0.2477-0.22420.18-0.0148-0.16870.40690.3936-0.03020.18380.1112-0.03270.3130.02360.22513.539821.6857157.6824
301.1967-0.08610.2380.89460.11931.332-0.00490.11040.0764-0.1679-0.0025-0.0945-0.09460.18070.01210.11380.00640.0160.1459-0.00350.12883.374734.136138.0588
312.3387-1.25810.02483.1888-0.26151.5048-0.01150.2177-0.157-0.35560.01460.16380.103-0.16860.0020.1913-0.018-0.03230.223-0.02360.1591-11.91120.7224123.2579
322.0631-0.08730.00132.0540.42691.604-0.05060.0977-0.0172-0.0992-0.00260.10840.0618-0.12080.02460.0943-0.0161-0.00220.1174-0.00210.0927-8.956824.2226131.9644
331.0767-0.261-0.26531.33440.72550.9355-0.06410.1349-0.1041-0.10170.1482-0.03780.06350.1787-0.0250.14890.01320.02090.1838-0.03450.1396-0.386322.8429126.7448
340.7975-0.5398-0.74812.34582.14032.052-0.16450.1779-0.0848-0.49830.2358-0.5455-0.1828-0.0644-0.03840.2834-0.0490.0810.2057-0.02940.22253.730530.5013121.7144
351.0549-0.14260.37411.15870.28671.6937-0.029-0.0840.0194-0.0224-0.01770.05810.0309-0.07150.02990.09310.0270.00770.11360.00280.1126-5.156430.159139.9366
369.0008-4.82571.04043.52050.91442.9988-0.0963-0.0561-0.2473-0.57320.15940.0067-0.28140.4034-0.03490.2794-0.15540.00940.30190.03270.299515.546610.080837.8236
370.5392-0.1873-0.25710.9054-0.56120.55320.0308-0.3258-0.0345-0.05420.05020.2365-0.0288-0.7604-0.19360.1807-0.16370.01110.57440.0330.2216-17.36195.58432.1605
381.1794-0.03750.68390.6705-0.58282.1938-0.00950.10280.0882-0.1222-0.02070.01470.1618-0.12570.05210.2126-0.05510.01010.1773-0.01730.1402-3.788210.015114.2611
390.7206-0.10350.40491.0105-0.36571.08750.02590.01450.0307-0.2679-0.07530.16020.2249-0.24170.06950.2562-0.071-0.00380.2079-0.02850.1764-3.13696.322520.0432
403.5124-2.2025-3.282.94593.71296.0017-0.1228-0.09460.23570.2471-0.0013-0.13130.07830.80230.04680.228-0.07030.00520.40230.11460.254715.75110.489728.4075
410.9947-0.08610.35620.9156-0.82010.87310.0506-0.1217-0.0533-0.14190.16160.21340.2952-0.4670.07750.2642-0.1734-0.01580.3771-0.00160.2098-10.3933-0.728237.0045
421.42230.2922-0.18841.3992-0.80960.77920.0974-0.3082-0.12920.1348-0.0576-0.06490.2975-0.18310.04730.3077-0.16010.0020.3324-0.00120.18641.1682-5.522652.6645
431.1637-0.31170.33031.5567-0.9920.6671-0.2016-0.666-0.07710.60120.03310.49610.1757-0.2126-0.28330.3924-0.10610.13430.54270.00850.2677-8.87771.223857.3941
441.7262-0.18480.67061.2029-0.70882.24150.00740.0348-0.0105-0.0008-0.00970.01380.2259-0.2174-0.00620.1875-0.09930.02450.2245-0.03110.13480.45151.693739.3162
452.0394-0.7181-0.28562.92430.39381.1808-0.0315-0.0423-0.2598-0.0511-0.13280.3361-0.0195-0.20810.0560.09470.0082-0.06250.15990.01020.119640.109610.3967145.4045
461.1378-0.34260.55350.9911-0.40411.99630.0176-0.2822-0.22370.08720.0156-0.02360.19530.1408-0.02150.14730.0267-0.01480.19850.06160.231653.8077-0.9836156.1327
470.4956-0.13380.01320.75230.64811.46310.01070.0397-0.0661-0.2747-0.14740.2114-0.164-0.2486-0.03910.20990.0525-0.08530.1452-0.04190.221241.03038.7725130.8634
481.29040.11-0.32030.86940.38940.799-0.0456-0.0424-0.0849-0.2135-0.10190.0891-0.2115-0.1580.04260.15820.0362-0.05360.1201-0.0130.193343.93211.512136.7403
498.68371.6204-1.77110.74850.03970.6835-0.176-0.03530.255-0.202-0.09720.1146-0.2306-0.0449-0.16760.1570.1006-0.07050.293-0.05810.214230.692826.3685143.4931
500.7777-0.00730.21861.1338-0.02361.4976-0.0194-0.1202-0.0701-0.04540.0064-0.12010.06150.21670.01670.13420.0132-0.00360.22190.0260.203859.234410.4169149.7686
510.9309-0.22450.01211.04490.13891.1918-0.0415-0.2747-0.16690.0116-0.01150.06390.0987-0.11140.05820.11750.0045-0.00490.23240.0370.191545.55238.3507158.7089
523.35510.3621-0.78381.8815-0.08961.61290.0389-0.6040.30510.2395-0.1325-0.0558-0.5042-0.03940.07920.26760.0447-0.03260.348-0.0550.187448.150229.0165172.6311
532.77640.10470.75621.9272-0.58920.4207-0.1463-0.14770.23160.051-0.0480.1688-0.3658-0.16040.13250.15270.0361-0.03410.2877-0.0370.130247.15624.3757163.9544
541.2357-0.17630.82011.16430.24440.9-0.0342-0.32820.01780.2201-0.01930.0093-0.0774-0.01470.05240.19970.0032-0.02430.33420.01910.158852.600518.081169.7641
550.6326-0.5959-0.37172.32342.11742.0304-0.0518-0.1538-0.07260.6305-0.4253-0.1726-0.26520.0408-0.61720.296-0.0697-0.08350.43080.19730.249747.355310.5463174.5848
561.6409-0.33680.24340.89960.54641.5924-0.0744-0.2334-0.02-0.0541-0.04610.1367-0.1425-0.15290.09040.10730.0456-0.02240.2033-0.00250.118744.991517.4825155.9054
570.92650.4678-0.33370.3335-0.29270.28140.0179-0.02480.36030.0018-0.0962-0.0025-0.12620.051-1.17220.1194-0.42840.27990.7070.01130.177148.343952.20323.1847
580.5164-0.739-0.34511.2870.01351.84070.0387-0.4012-0.24550.1241-0.1616-0.03060.30020.17470.09770.2082-0.06780.0020.26470.01730.109433.844726.802536.2619
590.7524-0.3081-0.52240.763-0.59311.53440.1385-0.0237-0.2331-0.0964-0.04210.03710.6852-0.237-0.00160.3069-0.1299-0.00370.2726-0.00870.200825.181721.340418.1639
600.3567-0.09850.11690.4803-0.28290.97010.0087-0.14350.00810.08940.00990.07540.0148-0.0955-0.00780.1556-0.06860.04250.2778-0.00020.162928.367638.024437.0528
610.85850.35130.22864.48320.6921.2628-0.0369-0.2334-0.09620.33060.1499-0.43020.0980.299-0.09690.209-0.025-0.03650.42650.00550.218447.696333.64852.5263
620.9215-0.44530.19834.55650.20581.80230.0708-0.13160.02440.1244-0.0224-0.44850.12720.2568-0.04440.1396-0.05820.01870.2999-0.00130.131843.772934.997543.5997
630.73750.27590.02851.6244-0.71931.08750.0445-0.2149-0.04250.07470.0121-0.01120.17750.0234-0.04890.23-0.06070.00750.34510.0320.143536.659530.177448.8828
640.0991-0.11750.18282.4711-2.43212.4634-0.2556-0.198-0.26610.4670.22860.5044-0.0658-0.35130.07730.2518-0.01540.08490.40660.03010.224129.358535.969853.33
650.43220.26860.15881.0084-0.02071.0519-0.0004-0.0865-0.05890.091-0.0087-0.06370.07350.16050.00710.1341-0.05560.02210.25440.0110.124137.718137.869835.0056
669.6812-4.5332-1.97044.79671.93612.4940.12-0.1920.4259-0.20510.0235-0.5279-0.22910.6203-0.18090.2836-0.17450.0240.4913-0.01890.269248.147952.225632.7748
670.8929-0.5901-0.54730.9747-0.28511.28110.0998-0.0950.0728-0.1227-0.15280.1673-0.0093-0.29850.02050.1454-0.04790.02380.22420.02640.141622.61539.130919.2194
680.65030.0852-0.90170.6166-0.57181.58630.0582-0.2486-0.00240.139-0.0730.24450.5036-0.5252-0.02330.2508-0.14950.05860.42040.01440.235516.264130.44436.9994
691.03120.1558-0.19450.5901-0.05211.59790.04960.0233-0.07490.0084-0.0468-0.04070.17730.08990.01360.1515-0.03480.02050.17910.0080.134833.54932.845618.5372
703.29240.57410.07991.00060.2372.129-0.02890.25760.2471-0.334-0.0121-0.1257-0.46890.08840.03280.24540.01570.05810.20290.06330.198830.672852.55883.3806
711.00070.71050.48811.0307-0.14241.32150.13040.08660.4158-0.2024-0.1084-0.0969-0.19260.0149-0.01910.1882-0.02670.05010.2060.01250.18531.710248.47812.2937
722.60660.15150.54131.48770.09141.52220.10130.12290.0931-0.1779-0.05460.00160.0003-0.0586-0.04360.1892-0.01970.01660.19150.01260.138926.372741.7596.874
730.8845-0.6957-0.23682.28230.12961.19440.12190.1184-0.0343-0.2039-0.12680.0932-0.02610.00990.01390.1186-0.02480.02750.1928-0.00560.136133.28338.309513.2122
741.8820.8764-0.00541.69960.26142.12370.0429-0.13730.1405-0.2259-0.10470.0801-0.2120.02760.010.1498-0.07250.01680.18510.00660.122433.328345.830224.8484
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 111 )
3X-RAY DIFFRACTION3chain 'A' and (resid 112 through 136 )
4X-RAY DIFFRACTION4chain 'A' and (resid 137 through 199 )
5X-RAY DIFFRACTION5chain 'A' and (resid 200 through 218 )
6X-RAY DIFFRACTION6chain 'A' and (resid 219 through 262 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 43 )
8X-RAY DIFFRACTION8chain 'B' and (resid 44 through 63 )
9X-RAY DIFFRACTION9chain 'B' and (resid 64 through 111 )
10X-RAY DIFFRACTION10chain 'B' and (resid 112 through 136 )
11X-RAY DIFFRACTION11chain 'B' and (resid 137 through 154 )
12X-RAY DIFFRACTION12chain 'B' and (resid 155 through 175 )
13X-RAY DIFFRACTION13chain 'B' and (resid 176 through 201 )
14X-RAY DIFFRACTION14chain 'B' and (resid 202 through 217 )
15X-RAY DIFFRACTION15chain 'B' and (resid 218 through 263 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 16 )
17X-RAY DIFFRACTION17chain 'C' and (resid 17 through 136 )
18X-RAY DIFFRACTION18chain 'C' and (resid 137 through 175 )
19X-RAY DIFFRACTION19chain 'C' and (resid 176 through 201 )
20X-RAY DIFFRACTION20chain 'C' and (resid 202 through 217 )
21X-RAY DIFFRACTION21chain 'C' and (resid 218 through 262 )
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 111 )
23X-RAY DIFFRACTION23chain 'D' and (resid 112 through 263 )
24X-RAY DIFFRACTION24chain 'E' and (resid 1 through 16 )
25X-RAY DIFFRACTION25chain 'E' and (resid 17 through 76 )
26X-RAY DIFFRACTION26chain 'E' and (resid 77 through 201 )
27X-RAY DIFFRACTION27chain 'E' and (resid 202 through 262 )
28X-RAY DIFFRACTION28chain 'F' and (resid 1 through 43 )
29X-RAY DIFFRACTION29chain 'F' and (resid 44 through 63 )
30X-RAY DIFFRACTION30chain 'F' and (resid 64 through 111 )
31X-RAY DIFFRACTION31chain 'F' and (resid 112 through 136 )
32X-RAY DIFFRACTION32chain 'F' and (resid 137 through 154 )
33X-RAY DIFFRACTION33chain 'F' and (resid 155 through 201 )
34X-RAY DIFFRACTION34chain 'F' and (resid 202 through 217 )
35X-RAY DIFFRACTION35chain 'F' and (resid 218 through 263 )
36X-RAY DIFFRACTION36chain 'G' and (resid 1 through 16 )
37X-RAY DIFFRACTION37chain 'G' and (resid 17 through 76 )
38X-RAY DIFFRACTION38chain 'G' and (resid 77 through 201 )
39X-RAY DIFFRACTION39chain 'G' and (resid 202 through 262 )
40X-RAY DIFFRACTION40chain 'H' and (resid 1 through 16 )
41X-RAY DIFFRACTION41chain 'H' and (resid 17 through 111 )
42X-RAY DIFFRACTION42chain 'H' and (resid 112 through 199 )
43X-RAY DIFFRACTION43chain 'H' and (resid 200 through 218 )
44X-RAY DIFFRACTION44chain 'H' and (resid 219 through 263 )
45X-RAY DIFFRACTION45chain 'I' and (resid 1 through 43 )
46X-RAY DIFFRACTION46chain 'I' and (resid 44 through 76 )
47X-RAY DIFFRACTION47chain 'I' and (resid 77 through 201 )
48X-RAY DIFFRACTION48chain 'I' and (resid 202 through 262 )
49X-RAY DIFFRACTION49chain 'J' and (resid 1 through 16 )
50X-RAY DIFFRACTION50chain 'J' and (resid 17 through 63 )
51X-RAY DIFFRACTION51chain 'J' and (resid 64 through 111 )
52X-RAY DIFFRACTION52chain 'J' and (resid 112 through 136 )
53X-RAY DIFFRACTION53chain 'J' and (resid 137 through 154 )
54X-RAY DIFFRACTION54chain 'J' and (resid 155 through 201 )
55X-RAY DIFFRACTION55chain 'J' and (resid 202 through 218 )
56X-RAY DIFFRACTION56chain 'J' and (resid 219 through 262 )
57X-RAY DIFFRACTION57chain 'K' and (resid 1 through 16 )
58X-RAY DIFFRACTION58chain 'K' and (resid 17 through 43 )
59X-RAY DIFFRACTION59chain 'K' and (resid 44 through 63 )
60X-RAY DIFFRACTION60chain 'K' and (resid 64 through 111 )
61X-RAY DIFFRACTION61chain 'K' and (resid 112 through 136 )
62X-RAY DIFFRACTION62chain 'K' and (resid 137 through 154 )
63X-RAY DIFFRACTION63chain 'K' and (resid 155 through 201 )
64X-RAY DIFFRACTION64chain 'K' and (resid 202 through 218 )
65X-RAY DIFFRACTION65chain 'K' and (resid 219 through 262 )
66X-RAY DIFFRACTION66chain 'L' and (resid 1 through 16 )
67X-RAY DIFFRACTION67chain 'L' and (resid 17 through 43 )
68X-RAY DIFFRACTION68chain 'L' and (resid 44 through 63 )
69X-RAY DIFFRACTION69chain 'L' and (resid 64 through 111 )
70X-RAY DIFFRACTION70chain 'L' and (resid 112 through 136 )
71X-RAY DIFFRACTION71chain 'L' and (resid 137 through 154 )
72X-RAY DIFFRACTION72chain 'L' and (resid 155 through 201 )
73X-RAY DIFFRACTION73chain 'L' and (resid 202 through 250 )
74X-RAY DIFFRACTION74chain 'L' and (resid 251 through 262 )

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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