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- PDB-4kb3: Crystal structure of the mitochondrial peroxiredoxin from Leishma... -

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基本情報

登録情報
データベース: PDB / ID: 4kb3
タイトルCrystal structure of the mitochondrial peroxiredoxin from Leishmania braziliensis in the decameric form
要素Peroxidoxin
キーワードOXIDOREDUCTASE / Thioredoxin-like / mitochondria
機能・相同性
機能・相同性情報


thioredoxin-dependent peroxiredoxin activity / thioredoxin-dependent peroxiredoxin
類似検索 - 分子機能
: / Peroxiredoxin, AhpC-type / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...: / Peroxiredoxin, AhpC-type / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
thioredoxin-dependent peroxiredoxin
類似検索 - 構成要素
生物種Leishmania braziliensis (ブラジルリーシュマニア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.93 Å
データ登録者Giuseppe, P.O. / Souza, T.A.C.B. / Morais, M.A.B. / Murakami, M.T.
引用ジャーナル: To be Published
タイトル: Crystal structure of the mitochondrial peroxiredoxin from Leishmania braziliensis in the decameric form
著者: Souza, T.A.C.B. / Morais, M.A.B. / Giuseppe, P.O. / Murakami, M.T.
履歴
登録2013年4月23日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年5月14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

ダウンロードとリンク

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集合体

登録構造単位
A: Peroxidoxin
B: Peroxidoxin
C: Peroxidoxin
D: Peroxidoxin
E: Peroxidoxin
F: Peroxidoxin
G: Peroxidoxin
H: Peroxidoxin
I: Peroxidoxin
J: Peroxidoxin


分子量 (理論値)分子数
合計 (水以外)213,87410
ポリマ-213,87410
非ポリマー00
00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area18630 Å2
ΔGint-108 kcal/mol
Surface area68580 Å2
手法PISA
単位格子
Length a, b, c (Å)90.212, 98.901, 228.138
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

#1: タンパク質
Peroxidoxin


分子量: 21387.377 Da / 分子数: 10 / 断片: UNP residues 34-225 / 由来タイプ: 組換発現
由来: (組換発現) Leishmania braziliensis (ブラジルリーシュマニア)
遺伝子: LBRM_23_0050 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: A4HCL7, 酸化還元酵素; 過酸化物を電子受容体にする; ペルオキシダーゼ

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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: 2.38 Å3/Da / 溶媒含有率: 48.3 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.4
詳細: 0.1 M MMT buffer pH 4.4, 13.9%w/v PEG 1,500, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: LNLS / ビームライン: W01B-MX2 / 波長: 1.459 Å
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2012年10月19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: 1.459 Å / 相対比: 1
反射解像度: 2.93→40 Å / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
反射 シェル
解像度 (Å)Diffraction-ID% possible all
2.93-3.11195.5
3.11-3.321100
3.32-3.591100
3.59-3.931100
3.93-4.391100
4.39-5.051100
5.05-6.161100
6.16-8.611100
8.61-40198.3

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解析

ソフトウェア
名称バージョン分類
MAR345dtbデータ収集
MOLREP位相決定
PHENIX(phenix.refine: 1.8_1069)精密化
XDSデータ削減
XDSデータスケーリング
精密化構造決定の手法: 分子置換 / 解像度: 2.93→19.98 Å / SU ML: 0.4 / σ(F): 2 / 位相誤差: 28.59 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.282 2256 5.07 %
Rwork0.231 --
obs0.234 44517 99.9 %
all-46773 -
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: 2.93→19.98 Å
タンパク質核酸リガンド溶媒全体
原子数12942 0 0 0 12942
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00613209
X-RAY DIFFRACTIONf_angle_d1.12217880
X-RAY DIFFRACTIONf_dihedral_angle_d15.1534868
X-RAY DIFFRACTIONf_chiral_restr0.0582007
X-RAY DIFFRACTIONf_plane_restr0.0062311
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-2.99350.38311440.36572612X-RAY DIFFRACTION100
2.9935-3.06290.38271480.33972563X-RAY DIFFRACTION100
3.0629-3.13920.33941480.32092605X-RAY DIFFRACTION100
3.1392-3.22380.39691370.31262620X-RAY DIFFRACTION100
3.2238-3.31820.32011420.28672610X-RAY DIFFRACTION100
3.3182-3.42480.32271340.26942616X-RAY DIFFRACTION100
3.4248-3.54660.27061400.24122599X-RAY DIFFRACTION100
3.5466-3.68770.2881320.24122641X-RAY DIFFRACTION100
3.6877-3.85440.29961340.23262610X-RAY DIFFRACTION100
3.8544-4.0560.27781530.20192635X-RAY DIFFRACTION100
4.056-4.30780.23641440.19762652X-RAY DIFFRACTION100
4.3078-4.63650.2581460.17342625X-RAY DIFFRACTION100
4.6365-5.09610.24771450.17872644X-RAY DIFFRACTION100
5.0961-5.81750.24861360.20472695X-RAY DIFFRACTION100
5.8175-7.27020.28441390.24492706X-RAY DIFFRACTION100
7.2702-19.97510.24881340.21572828X-RAY DIFFRACTION100
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)
14.14421.4491-3.98518.7485-3.92527.3261-0.56310.974-0.6575-0.94220.3324-0.09740.1987-0.08520.33990.7227-0.03680.10370.77620.00390.7141-22.6134-8.3823-25.2158
29.4429-3.05150.46955.92370.26051.63180.32280.47391.20880.5627-0.2474-0.7562-0.75140.16290.06840.7505-0.070.06050.4817-0.00780.5297-37.38117.438-26.5433
32.0918-1.3173.92123.9452.62689.4897-0.0583-0.98850.4674-1.0198-0.3078-0.35340.36510.0970.3270.9315-0.30370.08160.5666-0.00830.5071-33.7844-0.1074-19.3366
46.88381.31142.46356.21031.16154.0647-0.4707-0.6361-0.24062.00120.76340.58781.6745-1.5295-0.34770.9589-0.15210.26061.037-0.28190.7816-52.6977-7.2081-22.6951
58.75440.04052.63981.1116-2.18324.24430.13350.1923-0.34070.0719-0.73590.34971.12010.60520.41251.1483-0.19130.19291.0156-0.0730.5581-45.9966-2.2941-12.3483
62.0932-3.79963.68448.2595.06266.3539-0.52590.59320.19651.5381-0.29180.2846-1.42330.4510.74741.4739-0.09030.31530.6540.02630.7021-36.48695.1566-8.7655
73.6549-1.90771.10041.4823-1.89563.2095-0.1661-0.1461-0.02550.11060.07870.1772-0.0464-0.71030.27180.6598-0.13910.1470.3884-0.14530.5574-49.47651.9456-22.0233
86.02112.84033.71333.2778-1.26455.93590.28780.0086-0.00050.5598-0.10890.0361-1.1493-1.01390.04971.1266-0.15510.17150.6497-0.12380.5147-45.49734.063-20.8467
98.090.66342.54966.841-2.44081.7817-0.78661.5284-0.7793-0.83230.3721-0.27561.13620.28620.28230.9951-0.02390.27870.6365-0.13150.5715-38.4575-7.5085-33.0527
102.98040.06291.56061.0311-0.15894.9960.08290.5963-0.32650.158-0.28440.03480.79940.22980.23410.7975-0.00060.09890.4996-0.04560.443-34.0806-8.1324-22.0344
112.23785.46080.96831.9842.94030.8294-0.8115-0.29510.0056-0.0079-0.05911.1106-0.5805-0.18670.6261.43710.07240.04870.57930.05830.623-39.1569-9.1262-11.5778
122.0746-3.07112.35869.37860.07552.064-0.4489-0.26520.66571.50940.4448-0.4178-1.62742.5732-0.06571.2166-0.2267-0.01661.2513-0.0920.6135-23.8377-2.704-8.7143
132.27121.98830.45582.01670.5775.14470.3862-0.7117-0.246-0.99480.13242.22490.755-0.2392-0.65141.13840.04750.09360.42010.01180.9299-35.7245-24.5824-26.6435
146.86060.40011.81462.6467-1.17534.9681-1.19860.1468-2.16910.62980.68520.57940.56690.62280.34571.59850.17870.20230.44190.14020.7802-25.0424-36.9517-14.5673
152.0393-5.0565-2.20118.6674-2.88682.0165-0.5374-1.9453-0.00620.55110.15931.59290.74610.38850.06371.20220.03010.26650.6157-0.08210.7156-35.5848-29.1705-14.2208
166.17210.55971.98722.49740.11530.65030.5521-0.66630.97290.8008-0.09530.276-0.48850.0673-0.66741.49780.14330.33381.13010.10740.6542-16.3077-20.1077-10.43
179.95590.3754-1.75582.36270.43216.6220.6116-0.960.00630.9855-0.23621.010.03110.6487-0.53881.4727-0.00110.30520.57750.13710.719-30.1896-24.9065-2.9387
183.0786-0.175-0.29181.33710.50436.56320.257-0.1983-0.11240.5595-0.32680.07821.11191.32150.09641.3820.04410.05730.49950.02480.4735-18.7517-28.7069-7.73
191.9977-6.9611-1.10699.8357-2.61835.01521.1446-0.01910.1975-1.7709-0.8961-0.43240.79970.7884-0.07020.97160.24760.12840.87550.09460.5415-19.4063-26.4288-25.2883
202.0172.00892.66481.9325-2.52642.7984-1.4290.04840.03810.1480.34370.25060.2180.02781.0861.0405-0.02410.18610.62150.04730.4531-21.5097-19.7041-24.7191
213.0301-0.50040.11732.7461-0.58492.1814-0.6038-0.0415-0.23320.22540.37320.40320.07310.15610.27060.88-0.05020.08710.4503-0.03850.5127-30.3122-20.5011-18.9406
223.87430.9978-0.7532.7717-0.90971.707-0.11730.287-0.14171.003-0.10580.0833-0.0083-0.61770.34431.18510.10750.19710.68010.00360.5247-32.3281-16.1123-9.1609
231.97675.0962-1.13747.493-5.45484.9672-0.77091.5455-0.91840.5748-0.20561.66540.8613-0.17780.52290.7744-0.13930.4620.5964-0.14331.2294-47.3221-23.5401-12.6015
245.17340.3821-0.82410.26340.75342.86990.0365-0.1545-1.28450.222-0.0468-1.44252.3229-0.09050.02711.0616-0.55570.43650.84450.0682.3822-57.1701-16.4401-15.5752
254.23330.67480.78051.80070.27510.1311-0.91010.6269-0.50480.08650.38950.06920.36241.09880.56091.960.1530.23711.44160.22210.69297.3633-24.7719-40.6665
264.3852-0.7088-0.68845.82874.39281.98920.2342-1.2764-0.26410.16320.4917-1.4425-0.52490.7014-0.411.11330.1902-0.0470.8547-0.00480.54332.2157-17.2775-22.2951
275.64510.609-1.71134.52160.36285.290.06350.986-0.08810.3958-0.1236-0.78330.71580.50830.13371.1704-0.0794-0.0591.28310.05940.92445.4387-13.6058-20.8738
282.16861.52990.60539.31951.46192.1386-0.6758-0.8231.85260.16791.0141-0.15980.25830.7932-0.57580.71830.0681-0.06940.9326-0.01050.77699.658-23.9749-25.7877
296.72080.4679-0.60123.2413.7575.8309-1.4686-1.5732-1.54612.26582.59060.9327-0.23920.1566-0.57441.5420.7043-0.02791.53320.07540.8045-3.7432-33.9737-14.3368
306.56193.2946-0.54655.78040.17391.2321-0.6082-1.94930.2729-2.1597-0.06120.53230.49630.04630.59120.99030.1958-0.06061.3810.04870.56713.5636-29.0706-16.0632
312.9741-1.2901-0.7483.0563-0.55332.4403-0.1759-0.6045-0.22531.10730.025-0.44310.13250.34940.16821.15720.1588-0.14941.05680.10220.51991.5784-25.1646-13.1155
322.038-5.5834-4.33792.08648.51338.6588-0.17871.8402-0.6354-0.5606-0.71070.0855-1.1436-1.07060.72670.99590.3272-0.03120.98110.030.5461-6.7473-22.7935-28.5211
332.05471.897-9.36532.1135-5.31759.4122-0.8744-0.33110.8956-1.70390.32240.13840.4597-0.9930.42810.88120.1149-0.09170.628-0.02220.5081-5.4953-29.1561-30.6988
343.53920.8027-1.09221.0358-0.20771.2648-0.1215-0.6446-0.5704-0.0693-0.0849-0.20920.34610.78530.15050.92670.27550.02810.75730.12690.59694.8729-29.5232-30.0756
353.97964.7442-0.56134.9452-0.7008-0.0208-1.1707-0.8413-0.4342-0.52450.1342-0.7830.57350.59060.93241.15940.49990.0480.98250.13370.862410.4029-37.167-23.1588
366.0579-0.4868-1.45267.1145-2.16142.1354-0.46520.57170.94240.04781.4580.4099-0.10130.5022-0.55610.87970.2841-0.01661.05980.00160.849621.4276-28.2035-31.1736
377.58943.05645.36741.98243.62694.1992-0.4669-0.24050.7518-0.61980.52331.8025-0.56670.2349-0.05551.05170.07450.07040.64150.04931.0053-5.3382-39.888-34.9118
386.1701-1.4474-1.71595.50661.06314.8392-0.5633-2.519-0.75650.6271.30190.36571.12820.5129-0.71780.88410.20050.01041.2086-0.00440.64787.6385-51.9986-49.1611
392-5.0291-3.80968.33343.7516.81860.0442-0.0192-1.6065-0.5958-0.15071.52750.7704-0.60860.51251.1449-0.1407-0.10330.73040.08111.12212.722-55.3116-45.9578
405.7166-1.3046-0.14522.1506-5.37922.2440.39070.29170.60860.439-0.20821.23121.05880.6540.21311.19630.12990.09830.61060.06890.69486.5721-48.3402-37.8985
419.82780.8232-4.8197.70512.36429.495-1.40970.1779-0.38331.0790.7765-1.1506-1.03052.35751.06850.92020.1726-0.18451.3679-0.00090.754521.6087-39.1539-48.5591
421.91870.3957-0.41570.3664-0.3712.5293-0.2999-0.6234-0.375-0.00230.13210.840.53881.14820.26131.17390.3834-0.05010.96320.27351.007719.0848-49.8566-36.4018
438.8458-3.4326.3111.9896-3.7212.01790.44020.3574-0.6969-0.06160.00641.06360.1117-0.2563-0.39681.11860.37320.12210.63270.17931.78029.7852-56.9529-31.6386
442.2346-1.1609-0.49724.3709-0.30311.0047-0.02070.73130.26790.42880.1519-0.39810.65131.308-0.2741.01510.5234-0.01051.31080.13180.67818.3845-48.6967-48.7959
456.0409-1.2147-1.75252.07231.51032.0304-0.1869-0.1463-0.1401-0.46520.01620.88360.20350.17120.16830.85570.3366-0.00090.84370.09780.62273.2562-39.6407-50.2791
464.62594.9804-4.21227.3658-4.93734.7584-0.3549-0.0312-0.02870.82331.0990.3647-0.421-0.9564-0.89220.76910.2329-0.00430.67220.18890.60997.0329-37.9761-43.0064
472.5609-1.6474-0.17622.281.35411.01120.0738-1.0637-0.26141.1258-0.1013-0.48620.07790.08830.00631.11270.2358-0.15011.07940.19710.61668.4258-42.8173-30.8208
481.6508-0.48760.04541.6248-0.67110.30840.552-0.07861.84940.6836-0.95370.97260.32980.02940.38781.0376-0.21380.07150.88310.13161.0941-1.4101-47.8963-15.7714
498.9899-1.22515.82289.13144.50047.01-0.21521.13050.70810.1058-2.1334-0.5993-0.0762-1.1241.63360.53890.1853-0.10731.3836-0.23640.66023.7944-24.5723-79.2215
508.0470.64862.33126.834-3.50849.257-0.3692-0.52340.93030.42650.6984-0.7794-1.51971.1415-0.21710.794-0.0447-0.03610.6616-0.12070.667820.9698-25.7951-66.3807
512.17691.7832-3.74788.9755-1.28382.4857-0.36130.31950.6456-0.11240.09210.4502-0.27791.49910.61040.6781-0.05-0.23590.5342-0.01210.606317.3335-29.8925-76.1293
527.29922.4323-2.38374.827-6.99642.0248-1.5454-0.0599-1.8981-0.93410.89520.76073.2375-0.16080.37771.35140.3626-0.00960.7822-0.0220.67717.6238-46.9051-64.7413
534.6151-0.6797-0.35436.0238-2.97738.5541-0.44440.7713-0.6423-0.2296-0.0946-0.73550.99750.50920.45880.53040.1628-0.01370.9351-0.12670.727825.5241-37.8647-78.4385
542.4733-2.79990.03733.1913-1.94891.9034-0.168-0.7828-0.52570.05960.06590.29720.77171.39420.0030.70170.3173-0.12240.8408-0.07290.650823.7487-39.4545-64.9217
550.78112.02070.81557.8468-1.82826.5068-0.4924-0.0474-0.5801-0.03840.2347-0.02740.09890.2909-0.02450.6090.03880.04410.80950.02410.556124.4074-35.4895-67.5503
564.5813.65522.76642.15480.68425.4459-0.3344-1.35710.93920.91960.13630.88910.1171-0.36010.29280.51360.25950.01090.9961-0.07730.65886.67-33.3574-64.0798
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843.56934.3790.66022.0194-2.6672.7886-1.75130.84361.47950.0635-0.6549-0.0101-2.0426-0.63841.1820.9254-0.2485-0.55070.48550.29581.4637-31.56162.309-102.6909
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904.2246-2.30860.01523.45960.68343.67-0.106-0.10420.531-0.1285-0.37470.1604-0.6049-0.12250.47710.60450.1607-0.0550.4965-0.05710.6096-54.4499-8.4145-92.7639
915.33333.82530.2439.2164.1311.9893-1.1457-0.32980.7154-0.59220.2392-0.3613-1.049-0.82090.81980.49460.05090.00730.5819-0.10890.4954-53.9133-13.3624-93.3539
925.18721.022-0.97762.2931-0.26254.68540.0761-1.03390.30420.90860.0259-1.2067-0.343-0.2336-0.0620.4986-0.0835-0.06760.5332-0.05170.5238-40.5283-11.9811-81.2963
932.26620.41991.33776.60691.13594.8534-0.33480.12770.24660.1780.6633-0.4009-0.29740.2076-0.31380.3920.00090.03280.424-0.03140.4098-38.0764-17.5183-93.017
942.1274.51051.69149.38463.66711.64010.0338-0.0962-0.3738-0.16280.1946-0.6588-0.6869-0.3544-0.13930.6899-0.0053-0.11860.45410.09020.5554-39.3365-10.7129-102.4927
956.3619-3.4852-1.06158.51241.35643.274-0.16771.3586-0.3785-0.3401-0.0266-0.37860.2755-0.5559-0.02010.4743-0.13760.03440.64640.01130.5091-38.4399-25.6054-104.9866
962.0378-2.6758-6.74142.15483.49142.07671.31470.80670.90020.6210.9027-1.9372-0.38041.3395-1.90260.9406-0.1270.18891.3389-0.26341.1945-30.4991-34.7839-108.8316
972.0265.6096-1.3162.03671.46075.5616-0.14880.48030.0335-0.1741.0367-1.72090.7315-0.2356-1.19610.67340.04110.07070.7238-0.16610.9579-44.20663.5553-53.9202
981.59541.21930.83821.6928-2.0038.575-0.6817-0.16440.5296-0.07350.0465-0.5739-0.6927-0.31310.55310.87020.1313-0.07680.4288-0.18510.7251-46.57239.7416-75.8963
997.4366-1.86992.98033.5574-2.88968.46070.8632-1.08530.96010.33060.9681-0.51131.11431.7546-1.25081.2369-0.46460.31440.8561-0.59570.9783-43.002212.6917-74.186
1003.1438-1.9648-2.12715.7229-0.42774.30780.4189-0.00920.59490.0396-0.6122-1.2892-1.10670.9141-0.2140.7917-0.674-0.091-4.5082-3.1062-0.3794-49.627812.0207-66.0702
1012.54922.46550.9413.45861.03543.99140.40860.80150.14510.0109-1.3341.8694-0.7618-2.63121.01320.88470.2864-0.00391.1022-0.3480.7694-60.5494-2.7261-78.626
1024.01351.07810.45071.07121.88454.0172-0.17491.38530.6236-0.7832-0.57370.0175-0.4253-0.57290.72480.75680.4699-0.18381.6362-0.29271.2159-63.76117.5374-72.866
1033.0658-0.1009-0.9591.41990.77514.0501-0.3875-0.00930.7305-0.2212-0.32060.6548-1.1792-0.95190.47090.76580.3042-0.17650.6254-0.27570.7803-56.91958.923-76.8412
1044.02295.6464-0.21597.7041-1.54546.4476-0.1131-0.6928-0.2091-0.1691-0.5447-0.80430.5351.05830.34180.48710.1097-0.0110.7235-0.1180.5836-45.1901-4.2677-69.2668
1052.1018-0.608-0.78045.07290.70491.3347-0.1248-0.0305-0.5170.8616-0.19890.610.2328-0.30760.07710.66590.06670.02930.5605-0.30970.6084-51.93121.2384-65.5227
1061.2671-0.3503-0.98851.2618-0.44931.9194-0.2828-0.21750.06140.11360.08290.2893-0.4697-0.60580.21370.70390.0835-0.02570.9553-0.24610.5527-56.77852.9099-61.4017
1076.87673.1342.16757.321-0.66318.48562.14611.38960.15481.491-1.31731.4928-1.4768-0.5855-0.64481.0020.23310.16311.0794-0.38170.7845-59.275312.4046-56.3976
1088.60184.18552.76247.9467-2.74153.72030.0858-1.49981.10331.0720.2256-0.1008-0.94350.3934-0.07261.1773-0.4935-0.27951.0756-0.98841.2092-54.035919.1235-49.0241
1094.2258-0.3572.62465.8809-5.83957.05990.4531.3762-1.41030.05690.0406-1.98431.41921.0675-0.02240.92840.10190.15740.54510.08891.0958-53.8067-13.1385-60.8667
1100.71571.1688-1.45331.0659-0.695.7979-0.5614-0.1573-0.5531-0.3271-0.54091.15031.36310.6790.20340.9773-0.35990.21550.8348-0.42180.9628-60.9551-14.645-39.0714
1111.40420.6991-1.26830.3625-0.62681.1650.0073-1.22310.2879-1.2667-0.746-0.3590.5735-0.00660.07451.731-0.2837-0.50560.7189-0.6222.1303-65.7753-18.813-48.0101
1122.34611.46040.37754.51651.27774.9332-0.0454-0.81410.75410.012-1.29831.1411-0.4222-2.50731.1250.6563-0.0522-0.04390.9436-0.27590.6236-58.9626-0.4373-41.7954
1132.49040.9291.77625.51151.0925.8534-0.33150.49820.46610.29930.94891.41251.2711-1.60260.0180.6455-0.04990.18021.847-0.78471.0834-71.1958-1.7435-45.6843
1142.2358-2.1738-0.97232.0633-0.12684.38430.8002-0.59780.37270.4508-0.3813-0.05380.2011-0.691-0.38150.7198-0.03080.34190.9505-0.28530.7107-62.3024-4.1283-35.5831
1151.0690.91232.38574.80613.62565.8863-1.8240.2376-0.0431-0.6902-0.79231.6588-1.0382-3.29450.9759-0.5859-1.0431.191.1902-0.07050.3162-64.747-3.0243-36.3296
1167.52461.378-0.73217.1306-2.8662.0614-0.75570.7475-0.80510.0302-0.469-0.19941.63770.10771.01930.6288-0.0050.12230.4873-0.12410.4976-48.8241-9.0421-44.7079
1172.00265.44777.81842.034-7.38832.032-0.96641.1211-1.1883-1.449-1.1981-1.92341.8960.64711.73920.9278-0.04280.34080.66540.0690.7411-44.096-0.7114-42.6259
1182.42360.43370.642-0.1258-0.18282.11530.0003-0.0833-0.57330.0007-0.17520.5032-0.0358-0.63470.17330.6018-0.00140.07410.7042-0.25950.657-58.1908-5.7011-53.8364
1190.8552-0.47832.07532.5765-0.71576.3005-0.48340.7669-0.6032-0.84810.52030.5258-1.6089-0.3124-0.0560.6655-0.04380.03231.1886-0.42680.8477-66.6169-0.6113-55.7273
1202.081-1.4065-1.98865.50492.30422.07511.1482-0.1468-1.1922-0.51030.21990.93671.5737-0.8041-0.93041.0648-0.2382-0.26322.3762-0.79221.0611-72.5085-12.1659-66.0127
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 36:41)
2X-RAY DIFFRACTION2(chain A and resid 42:64)
3X-RAY DIFFRACTION3(chain A and resid 65:72)
4X-RAY DIFFRACTION4(chain A and resid 73:81)
5X-RAY DIFFRACTION5(chain A and resid 82:91)
6X-RAY DIFFRACTION6(chain A and resid 92:98)
7X-RAY DIFFRACTION7(chain A and resid 99:126)
8X-RAY DIFFRACTION8(chain A and resid 127:136)
9X-RAY DIFFRACTION9(chain A and resid 137:150)
10X-RAY DIFFRACTION10(chain A and resid 151:176)
11X-RAY DIFFRACTION11(chain A and resid 177:186)
12X-RAY DIFFRACTION12(chain A and resid 187:198)
13X-RAY DIFFRACTION13(chain B and resid 36:44)
14X-RAY DIFFRACTION14(chain B and resid 45:64)
15X-RAY DIFFRACTION15(chain B and resid 65:70)
16X-RAY DIFFRACTION16(chain B and resid 71:81)
17X-RAY DIFFRACTION17(chain B and resid 82:98)
18X-RAY DIFFRACTION18(chain B and resid 99:136)
19X-RAY DIFFRACTION19(chain B and resid 137:144)
20X-RAY DIFFRACTION20(chain B and resid 145:150)
21X-RAY DIFFRACTION21(chain B and resid 151:175)
22X-RAY DIFFRACTION22(chain B and resid 176:189)
23X-RAY DIFFRACTION23(chain B and resid 190:197)
24X-RAY DIFFRACTION24(chain B and resid 198:204)
25X-RAY DIFFRACTION25(chain C and resid 36:41)
26X-RAY DIFFRACTION26(chain C and resid 42:52)
27X-RAY DIFFRACTION27(chain C and resid 53:64)
28X-RAY DIFFRACTION28(chain C and resid 65:72)
29X-RAY DIFFRACTION29(chain C and resid 73:81)
30X-RAY DIFFRACTION30(chain C and resid 82:98)
31X-RAY DIFFRACTION31(chain C and resid 99:136)
32X-RAY DIFFRACTION32(chain C and resid 137:144)
33X-RAY DIFFRACTION33(chain C and resid 145:150)
34X-RAY DIFFRACTION34(chain C and resid 151:176)
35X-RAY DIFFRACTION35(chain C and resid 177:185)
36X-RAY DIFFRACTION36(chain C and resid 186:197)
37X-RAY DIFFRACTION37(chain D and resid 36:41)
38X-RAY DIFFRACTION38(chain D and resid 42:55)
39X-RAY DIFFRACTION39(chain D and resid 56:64)
40X-RAY DIFFRACTION40(chain D and resid 65:72)
41X-RAY DIFFRACTION41(chain D and resid 73:81)
42X-RAY DIFFRACTION42(chain D and resid 82:95)
43X-RAY DIFFRACTION43(chain D and resid 96:100)
44X-RAY DIFFRACTION44(chain D and resid 101:136)
45X-RAY DIFFRACTION45(chain D and resid 137:145)
46X-RAY DIFFRACTION46(chain D and resid 146:164)
47X-RAY DIFFRACTION47(chain D and resid 165:195)
48X-RAY DIFFRACTION48(chain D and resid 196:204)
49X-RAY DIFFRACTION49(chain E and resid 36:41)
50X-RAY DIFFRACTION50(chain E and resid 42:64)
51X-RAY DIFFRACTION51(chain E and resid 65:72)
52X-RAY DIFFRACTION52(chain E and resid 73:81)
53X-RAY DIFFRACTION53(chain E and resid 82:98)
54X-RAY DIFFRACTION54(chain E and resid 99:126)
55X-RAY DIFFRACTION55(chain E and resid 127:136)
56X-RAY DIFFRACTION56(chain E and resid 137:150)
57X-RAY DIFFRACTION57(chain E and resid 151:164)
58X-RAY DIFFRACTION58(chain E and resid 165:184)
59X-RAY DIFFRACTION59(chain E and resid 185:193)
60X-RAY DIFFRACTION60(chain E and resid 194:198)
61X-RAY DIFFRACTION61(chain F and resid 36:41)
62X-RAY DIFFRACTION62(chain F and resid 42:58)
63X-RAY DIFFRACTION63(chain F and resid 59:72)
64X-RAY DIFFRACTION64(chain F and resid 73:81)
65X-RAY DIFFRACTION65(chain F and resid 82:95)
66X-RAY DIFFRACTION66(chain F and resid 96:101)
67X-RAY DIFFRACTION67(chain F and resid 102:128)
68X-RAY DIFFRACTION68(chain F and resid 129:136)
69X-RAY DIFFRACTION69(chain F and resid 137:150)
70X-RAY DIFFRACTION70(chain F and resid 151:175)
71X-RAY DIFFRACTION71(chain F and resid 176:189)
72X-RAY DIFFRACTION72(chain F and resid 190:198)
73X-RAY DIFFRACTION73(chain G and resid 36:44)
74X-RAY DIFFRACTION74(chain G and resid 45:64)
75X-RAY DIFFRACTION75(chain G and resid 65:72)
76X-RAY DIFFRACTION76(chain G and resid 73:81)
77X-RAY DIFFRACTION77(chain G and resid 82:97)
78X-RAY DIFFRACTION78(chain G and resid 98:124)
79X-RAY DIFFRACTION79(chain G and resid 125:136)
80X-RAY DIFFRACTION80(chain G and resid 137:148)
81X-RAY DIFFRACTION81(chain G and resid 149:154)
82X-RAY DIFFRACTION82(chain G and resid 155:176)
83X-RAY DIFFRACTION83(chain G and resid 177:189)
84X-RAY DIFFRACTION84(chain G and resid 190:198)
85X-RAY DIFFRACTION85(chain H and resid 36:44)
86X-RAY DIFFRACTION86(chain H and resid 45:64)
87X-RAY DIFFRACTION87(chain H and resid 65:81)
88X-RAY DIFFRACTION88(chain H and resid 82:90)
89X-RAY DIFFRACTION89(chain H and resid 91:98)
90X-RAY DIFFRACTION90(chain H and resid 99:127)
91X-RAY DIFFRACTION91(chain H and resid 128:136)
92X-RAY DIFFRACTION92(chain H and resid 137:152)
93X-RAY DIFFRACTION93(chain H and resid 153:176)
94X-RAY DIFFRACTION94(chain H and resid 177:184)
95X-RAY DIFFRACTION95(chain H and resid 185:195)
96X-RAY DIFFRACTION96(chain H and resid 196:204)
97X-RAY DIFFRACTION97(chain I and resid 36:41)
98X-RAY DIFFRACTION98(chain I and resid 42:55)
99X-RAY DIFFRACTION99(chain I and resid 56:61)
100X-RAY DIFFRACTION100(chain I and resid 62:72)
101X-RAY DIFFRACTION101(chain I and resid 73:81)
102X-RAY DIFFRACTION102(chain I and resid 82:90)
103X-RAY DIFFRACTION103(chain I and resid 91:137)
104X-RAY DIFFRACTION104(chain I and resid 138:150)
105X-RAY DIFFRACTION105(chain I and resid 151:164)
106X-RAY DIFFRACTION106(chain I and resid 165:183)
107X-RAY DIFFRACTION107(chain I and resid 184:193)
108X-RAY DIFFRACTION108(chain I and resid 194:198)
109X-RAY DIFFRACTION109(chain J and resid 36:41)
110X-RAY DIFFRACTION110(chain J and resid 42:59)
111X-RAY DIFFRACTION111(chain J and resid 60:66)
112X-RAY DIFFRACTION112(chain J and resid 67:81)
113X-RAY DIFFRACTION113(chain J and resid 82:98)
114X-RAY DIFFRACTION114(chain J and resid 99:122)
115X-RAY DIFFRACTION115(chain J and resid 123:136)
116X-RAY DIFFRACTION116(chain J and resid 137:148)
117X-RAY DIFFRACTION117(chain J and resid 149:154)
118X-RAY DIFFRACTION118(chain J and resid 155:176)
119X-RAY DIFFRACTION119(chain J and resid 177:193)
120X-RAY DIFFRACTION120(chain J and resid 194:198)

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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