[日本語] English
万見
- PDB-3fm5: X-ray crystal structure of transcriptional regulator (MarR family... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 3fm5
タイトルX-ray crystal structure of transcriptional regulator (MarR family) from Rhodococcus sp. RHA1
要素Transcriptional regulator
キーワードTRANSCRIPTION REGULATOR / Transcriptional regulator / MCSG / PF04017 / PSI / MarR / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics
機能・相同性
機能・相同性情報


response to stress / DNA-binding transcription factor activity / metal ion binding
類似検索 - 分子機能
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
Transcriptional regulator
類似検索 - 構成要素
生物種Rhodococcus jostii (バクテリア)
手法X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 2 Å
データ登録者Nocek, B. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
引用ジャーナル: To be Published
タイトル: X-ray crystal structure of transcriptional regulator (MarR family) from Rhodococcus sp. RHA1
著者: Nocek, B. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
履歴
登録2008年12月19日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02009年2月3日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Source and taxonomy / Version format compliance
改定 1.22024年11月20日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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

-
集合体

登録構造単位
A: Transcriptional regulator
B: Transcriptional regulator
C: Transcriptional regulator
D: Transcriptional regulator
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)65,79210
ポリマ－65,4244
非ポリマー3686
水5,296294
1
A: Transcriptional regulator
C: Transcriptional regulator
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,8284
ポリマ－32,7122
非ポリマー1162
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-33.4 kcal/mol
Surface area13190 Å2
手法PISA
2
B: Transcriptional regulator
D: Transcriptional regulator
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,9636
ポリマ－32,7122
非ポリマー2524
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-34.7 kcal/mol
Surface area13840 Å2
手法PISA
3


  • 登録構造と同一
  • ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10450 Å2
ΔGint-74.1 kcal/mol
Surface area25160 Å2
手法PISA
単位格子
Length a, b, c (Å)75.114, 75.114, 213.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDモデル要素
11B-234-

HOH

21C-190-

HOH

-
要素

-
タンパク質 , 1種, 4分子 ABCD

#1: タンパク質
Transcriptional regulator


分子量: 16355.884 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Rhodococcus jostii (バクテリア) / 株: RHA1 / 遺伝子: RHA1_ro05125 / プラスミド: pET15b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): B834(DE3) / 参照: UniProt: Q0S6D0

-
非ポリマー , 5種, 300分子

#2: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O3
#3: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C2H6O2
#4: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Mg
#5: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Cl
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 294 / 由来タイプ: 天然 / 式: H2O

-
詳細

Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.3 Å3/Da / 溶媒含有率: 46.58 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5
詳細: 0.2M Mg(OAC), 20% PEG 3350, 4% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 19-ID / 波長: 0.9794 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2007年1月28日 / 詳細: Mirrors
放射モノクロメーター: Double crystal / 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: 0.9794 Å / 相対比: 1
反射解像度: 1.96→40 Å / Num. obs: 44238 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / 冗長度: 12.2 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 23.7
反射 シェル解像度: 1.96→1.99 Å / 冗長度: 6.8 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 3 / Num. unique all: 2024 / % possible all: 91.9

-
解析

ソフトウェア
名称分類
SBC-Collectデータ収集
HKL-3000位相決定
SHELXD位相決定
Cootモデル構築
MLPHARE位相決定
PHENIXモデル構築
PHENIX精密化
HKL-3000データ削減
HKL-3000データスケーリング
PHENIX位相決定
精密化構造決定の手法: 単波長異常分散 / 解像度: 2→37.136 Å / SU ML: 0.31 / σ(F): 1.89 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
Rfactor反射数%反射Selection details
Rfree0.2398 2198 4.99 %RANDOM
Rwork0.1941 ---
all0.21 43756 --
obs0.1964 41566 95.85 %-
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 / Bsol: 52.7 Å2 / ksol: 0.336 e/Å3
精密化ステップサイクル: LAST / 解像度: 2→37.136 Å
タンパク質核酸リガンド溶媒全体
原子数4072 0 22 294 4388
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0044174
X-RAY DIFFRACTIONf_angle_d0.7065647
X-RAY DIFFRACTIONf_dihedral_angle_d14.6831553
X-RAY DIFFRACTIONf_chiral_restr0.047672
X-RAY DIFFRACTIONf_plane_restr0.002753
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02530.33641330.2564248789
2.0253-2.0520.26851420.2312250691
2.052-2.08010.23571560.2253249390
2.0801-2.10980.27361240.2141255892
2.1098-2.14130.2861340.2222253891
2.1413-2.17480.25121260.2187252792
2.1748-2.21040.28331600.2112250390
2.2104-2.24850.21931460.2055254193
2.2485-2.28940.2131240.1983251191
2.2894-2.33340.27711380.2009255791
2.3334-2.38110.23971260.2269256393
2.3811-2.43280.25751030.2196274797
2.4328-2.48940.27131290.2203271898
2.4894-2.55160.2281540.22270498
2.5516-2.62060.26621270.2191275498
2.6206-2.69770.24041230.2251276699
2.6977-2.78470.31311520.2203275699
2.7847-2.88420.21371650.2118273699
2.8842-2.99970.28041800.21372742100
2.9997-3.13610.2651710.2192753100
3.1361-3.30140.23261260.20392771100
3.3014-3.50810.22191530.18492759100
3.5081-3.77870.20081770.16182752100
3.7787-4.15850.19481060.1522807100
4.1585-4.75920.18561450.14522783100
4.7592-5.9920.22761390.17222772100
5.992-37.1420.25191130.1805274297
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-7.13686.00217.69316.6677-3.03867.88190.61630.6769-1.8671-0.71140.1635-2.48740.55052.0676-0.75350.41950.1320.11320.5736-0.20161.125513.076228.8289101.1365
21.0620.99110.25080.94150.83880.4366-0.06940.1223-0.34850.25210.0719-0.68710.21830.1169-0.04170.3877-0.0431-0.0120.2782-0.03620.43453.610632.341898.814
37.415-0.96052.78440.2773-0.83472.085-0.032-0.7259-0.2903-0.09340.15920.03550.0786-0.3217-0.11280.3516-0.0450.03870.2871-0.01210.2953-7.044538.2889100.4416
48.606-2.2637-4.60748.85937.16811.4386-0.7062-2.38280.76872.15370.3644-0.7140.41331.0120.2090.45840.0975-0.03980.6869-0.08080.282-17.171343.6082100.2125
51.97955.01182.97331.2546.07538.48420.03130.60241.28740.2891-1.4220.61780.4732-1.98181.19470.421-0.08550.03920.971-0.10250.4651-24.027842.375898.3978
61.99143.863-1.71286.6396-5.12892.13380.2326-0.94-0.44640.4204-1.71060.40530.4972-0.00021.12950.4716-0.08390.07960.8301-0.08720.4307-20.383136.002293.5962
71.9162-5.14032.09356.3813-3.38288.6346-0.1862-1.23080.6809-1.69960.87250.6463-0.5621-3.1971-0.39040.5146-0.2867-0.08651.1313-0.16110.4834-23.707636.592985.639
86.6642-4.4714.84471.7674-6.98039.85170.94132.9947-0.3536-0.4739-0.93930.95410.66382.85630.18790.89110.0012-0.20521.7836-0.28920.7329-25.874734.878478.4174
9-0.6327-0.9204-1.3243.4372-1.1032-2.3445-0.51540.3726-0.87-0.72790.92690.3918-0.1515-0.246-0.19811.3398-0.4790.56391.2498-0.4811.3056-23.828325.3685.9713
102.10594.50622.02992.1119-8.53981.8958-0.96760.2494-3.85992.7668-2.9459-0.04762.0238-1.0483.60231.6067-0.54410.48260.7456-0.24781.309-19.442225.683891.2993
112.0125.6809-6.60177.929-2.95915.2503-0.95860.1104-1.5082-0.0319-0.2421.09411.1499-2.45041.00671.0144-0.39290.28180.9880.01591.04-27.193627.748194.4317
122.1053-8.68123.86619.54212.00752.04190.09962.0326-2.82270.55441.58022.7104-0.905-2.0428-1.64670.5318-0.24120.00181.5458-0.08711.0248-33.161935.960593.9631
135.7059-0.88423.5261.3839-0.54737.4184-0.0477-2.4551.1153-1.2257-0.17950.13280.2694-3.21050.31520.5224-0.3914-0.05041.1508-0.29150.7372-33.553734.498987.44
141.2908-3.18231.6161-5.6212-2.60481.79320.4827-0.0343-0.1488-1.0478-0.53032.4791-0.8043-0.87690.00830.6022-0.1313-0.19530.9886-0.10331.0239-31.866540.627584.551
158.80962.74957.41939.2885-8.56441.4393-1.14411.38611.4044-1.24510.2520.38130.1312-2.05390.60450.44260.1038-0.06721.43060.14340.5679-24.481145.907287.0091
160.71541.11213.80871.9896-0.0241.6854-0.6670.83481.195-0.14610.5432-0.551-0.222-0.71880.18570.36270.0342-0.00660.49810.11960.814-13.944547.362792.9645
177.7118-2.52474.08417.84982.912-7.9386-0.06331.21262.3777-1.7692-0.6542.5069-0.361-0.60660.42170.3835-0.01050.07720.0999-0.1440.7512-5.61947.920395.5649
182.8406-5.655-1.16322.65290.8959-5.9683-0.06061.61120.0993-1.1617-0.390.1162-0.2604-0.46840.28830.3237-0.09450.00460.41780.06070.22381.173647.059886.9054
193.59481.70762.52410.976-0.4394-7.7403-0.0046-0.0913-0.44420.1725-0.20710.24140.1957-0.46740.19480.376-0.11820.00370.4498-0.00120.2248-1.777840.110685.4835
205.95277.20013.7455.8333-7.15593.1963-0.82510.9338-0.1707-3.02050.44190.42880.93210.0162-0.04890.6312-0.16340.01510.4277-0.15050.2565-4.613931.092183.5015
217.4617-4.71534.99097.05182.26987.30431.46121.8901-1.3812-1.8794-0.3992-0.0177-0.28660.9704-1.00920.54830.14510.03620.5352-0.23360.4864-12.7883-4.85593.3303
222.5515-0.2546-1.70012.54211.15611.32890.0139-0.1222-0.1263-0.1581-0.0696-0.10130.2150.1030.0430.2956-0.01460.03170.3098-0.04430.2888-17.69581.9694103.1184
23-0.77250.01070.12070.8761-0.37564.48240.3066-0.1084-0.25990.1599-0.10880.3398-0.0262-0.68220.00790.2349-0.04420.01280.2926-0.05620.2745-25.09626.0678116.4695
242.3615-0.4004-1.66522.52970.35172.91940.24570.28070.0726-0.0698-0.06530.2959-0.4937-0.5512-0.1610.29810.0160.03370.35890.00180.2617-26.963114.714116.9981
258.0888-7.1589-3.68572.2767-1.00559.83820.356-0.48221.2280.91550.6737-2.7951-2.21551.318-0.94910.8915-0.26190.23320.4275-0.09110.6995-19.430726.7209117.1256
260.40112.24811.33258.61646.00632.23870.5385-0.25460.877-0.4130.7240.944-3.4421.0532-1.16421.2212-0.13010.32320.71980.24060.7155-24.141731.1074110.4103
276.9664-1.58729.64932.2657-0.30274.13571.60820.6439-0.2065-0.304-0.25840.38381.394-1.8713-0.83290.59640.0520.14910.57870.08860.4336-24.50821.5113105.0554
28-3.74073.23860.68220.0331-3.87292.12890.66110.84840.2366-0.09630.78380.9106-0.1159-2.4357-1.17480.43550.1682-0.00920.7820.12140.4856-32.365221.8568107.0958
295.7622.0287-0.8591.75371.60711.83340.62530.5119-0.0164-0.67610.06410.93360.1818-1.2196-0.45350.54360.16320.09420.57270.02420.5443-34.178823.0407116.1906
306.5671.1447-0.1612.6325-6.17197.7680.4954-0.34620.74660.86060.28461.0937-0.9142-1.2566-0.71450.64710.17490.19030.36770.13320.4485-33.193825.0967120.0319
311.97558.40827.22117.12541.92361.9423-1.3635-1.06983.1248-1.25430.41922.1979-1.30340.34020.96621.0718-0.0189-0.0820.69750.14011.2438-29.732539.6934111.5721
328.7840.18795.8525.2473-2.81033.4840.1698-1.13050.53230.1509-0.56461.5503-1.6494-1.41080.74960.85590.49890.11410.3830.16921.0331-28.98734.1992108.81
338.2428-3.80031.6952.10354.45828.95280.5793-1.49740.42390.6590.1363-0.7243-2.46420.0584-0.89790.7332-0.01040.1750.3434-0.10190.3284-25.575426.0773124.9848
341.2787-4.90979.91793.43977.13648.2015-0.5179-0.73810.6271.38930.7063-1.7969-0.27430.2555-0.00210.555-0.06950.08220.4310.00920.3823-22.812518.2545126.1217
353.19560.0459-6.50260.6305-0.45695.4038-0.2906-0.9863-0.59010.1478-0.0738-0.11870.1531.0870.22230.325-0.0612-0.01570.48140.02540.3738-17.98649.2448121.2784
364.3421-2.63447.30962.2187-3.4188.44311.11290.1462-1.4732-0.45820.96422.94151.6259-0.2936-1.54980.57240.04180.02840.43830.15850.7713-14.29820.5462117.1207
375.2449-2.22840.32175.3006-2.80622.5455-0.4367-1.6192-0.04851.2836-0.1575-0.80910.28640.1290.46680.4540.0455-0.02040.4362-0.00650.5404-4.62083.4404114.3599
380.4666-8.35522.50391.1493-1.93623.15490.938-0.2335-0.0910.5959-0.6247-0.4796-0.19520.2754-0.25210.2849-0.0758-0.09690.4206-0.01420.5781-6.22989.8968109.5442
397.3296-0.90860.19742.0243-1.2611.49370.27240.2758-0.0903-0.3838-0.58570.2981-0.2903-0.01670.22260.2909-0.03480.08360.3255-0.05740.5019-9.342814.7572103.6602
406.6663-0.5031.63593.4775-7.80342.0055-0.6826-0.764-0.18040.6015-1.19390.3109-1.64450.87360.90540.74050.16140.19960.3488-0.19640.4945-12.677621.3057104.9594
419.6373-6.63937.87169.5928-2.5283-2.23461.14323.45591.6-1.7584-0.1995-0.039-1.12540.9721-0.55220.6168-0.07280.01050.84730.18420.3804-14.44838.994882.9734
426.70780.4985-0.44368.2463-1.4110.9586-0.13220.29410.1940.4429-0.20850.11430.1171-0.24020.32520.3432-0.05950.00110.33190.00110.3555-9.608935.727690.7275
431.9408-4.28962.02351.2054-7.27161.97740.5869-0.5224-1.7729-0.96310.37210.54071.1095-0.8994-0.69620.4389-0.11980.03380.3142-0.02770.395-6.560126.847192.3526
445.0512-2.87633.96515.32992.69862.1913-0.814-0.85470.68230.2840.9277-0.6171-0.976-0.1669-0.12490.3436-0.0590.10150.20260.03560.3701-3.043520.383899.0153
455.80071.573-0.2303-4.85810.83231.7597-0.1038-0.2718-0.88240.047-0.0979-0.1281-0.1492-0.05290.15350.3874-0.0180.11130.2433-0.00340.4983-0.138318.9455105.798
46-3.94042.09491.50124.91611.69730.5651-0.15810.6515-0.4454-0.15980.0559-0.3382-0.03720.31770.07130.3062-0.04540.00560.2451-0.01140.44867.33327.1306109.3396
475.3631-2.6196-5.9623-2.6870.77379.83550.58440.26770.3148-0.5798-0.61010.0002-2.2945-0.2442-0.01480.9187-0.0247-0.08940.5296-0.01790.603412.671832.8267115.8267
482.12314.88589.6735-5.05228.81582.32040.3634-2.32780.43870.8361-1.02-0.25751.4453-4.16450.58010.6591-0.1195-0.07790.6739-0.06630.41342.635536.7575115.6247
493.61643.541-2.16613.3206-2.82692.2179-0.18020.0463-0.5650.847-0.15570.1611-0.1581-0.14990.30440.5521-0.03180.0620.3787-0.0510.4726-2.786433.9679112.9084
502.1501-9.7359-6.56352.39020.90530.029-0.8074-0.3532-0.25982.30710.44760.1825-0.2091-0.5480.43680.3762-0.00930.03630.32290.03220.5102-1.87127.3018117.5945
512.2747-5.0382-6.12588.7741.6122.8148-0.5953-0.2756-0.99012.51240.71490.7557-0.4154-1.9227-0.08430.6433-0.02980.04330.53250.17310.53332.81719.0766118.2235
523.0652-3.5782-0.49726.3431.80944.6008-0.3946-0.9851.06711.20130.2793-0.5249-0.3064-0.16380.09720.76280.1137-0.17840.4181-0.06790.52658.212824.1548120.5843
533.1754-2.51241.02466.6705-2.70529.52910.7765-0.3427-0.1941-1.30330.44430.10410.57731.7478-1.3221.5645-0.0637-0.13461.075-0.3490.897711.249636.4871125.1247
543.23134.57491.6588.33068.48398.6191-0.23990.1829-0.6322-0.07980.2931-0.93840.17261.4552-0.25130.3637-0.0322-0.12680.4672-0.03020.483412.123625.3535117.5002
555.66951.34179.73390.24553.74924.7177-0.78811.74390.9910.06470.8161-0.00251.13491.4257-0.07080.24370.15960.05060.1990.04010.793312.853218.2631111.5617
56-0.64232.10226.08084.53-1.06788.0584-0.12320.8273-2.544-1.62940.532-0.52720.21281.7861-0.32770.1735-0.05980.11560.3992-0.02680.589310.978620.3025105.351
572.3763-0.1366-2.4925-0.3839-1.98865.62-0.19350.1517-0.6658-0.1569-1.0428-0.02990.5437-0.05760.9860.3505-0.02880.13590.2509-0.07360.57256.48920.751796.8348
589.89721.7102-9.23692.123-6.585-3.0947-0.2486-2.1416-0.441-1.8598-0.3317-1.39532.05161.82540.35590.7769-0.0380.25380.5919-0.09380.492.406822.790388.7762
591.8859-2.2313-4.88842.76644.73252.1474-0.3559-0.0937-0.04430.5267-0.10840.03740.75780.96250.29580.5761-0.09340.10870.4642-0.11870.33978.082433.293485.9105
603.13682.33490.0572.71382.2203-0.5726-0.0277-0.301-0.04430.14310.1885-0.64130.07980.107-0.13990.396-0.08170.01170.2688-0.01980.3084.045140.157597.1699
615.91645.52961.68346.55533.02940.5770.5028-1.14220.04140.109-0.3107-0.3515-0.4230.0267-0.15080.386-0.05560.0720.4572-0.03980.4423-14.618716.1449113.7372
624.21880.0694.39330.40642.31519.1445-0.0725-0.20310.6619-0.2495-0.261-0.1055-0.7284-0.45650.17170.30790.02270.07280.2707-0.00550.3133-18.687911.365599.1665
635.3354-0.9838-4.4743-1.11965.0802-1.1361-0.31382.01420.1687-0.56670.24110.8934-1.1865-1.9070.01580.66510.01870.00570.81130.16780.2465-24.88075.937185.4703
646.99622.93395.00723.5417-4.1397-4.3966-0.28310.91120.23540.16310.00630.4317-0.25940.240.12830.41680.083-0.01440.5216-0.05610.303-24.04750.281492.2297
655.898-4.5847-8.54397.41674.06594.2427-0.0260.3442-0.7090.16850.8332-0.30751.47550.2468-0.53340.36120.1556-0.06040.4538-0.14220.2711-20.7102-8.086490.0511
662.0232-8.9089-4.06579.04599.0893.68310.16151.5317-3.40081.9329-0.2598-0.50541.757-0.3580.11361.21680.0381-0.36310.6277-0.25631.0028-22.2119-16.470890.7697
670.33740.42131.44932.0845-2.96563.20280.96110.3797-0.60310.69620.3806-0.02922.0984-1.8548-1.09970.6423-0.2213-0.16180.5960.06480.4391-26.859-10.55699.3923
682.1785-0.1006-1.28842.47174.41817.30440.7932-0.3145-0.1720.0028-0.7287-0.08-0.6648-1.5504-0.00650.320.01870.04950.5408-0.05990.2735-27.3767-5.1874100.8846
69-3.85083.42863.92071.64952.37396.16550.20680.43850.4915-0.3772-0.81330.3959-0.7912-1.09720.56260.23950.10750.00070.5092-0.11720.3263-33.2757-5.27594.4433
701.36880.08552.3583-0.10640.48914.7660.10360.1050.5138-0.23520.02990.0344-0.5177-0.7666-0.0570.4020.2404-0.11780.6593-0.08440.2543-31.5258-4.925183.9125
714.18412.65492.17959.1915-4.07844.51390.1395-1.6421-1.47670.49470.4669-0.9930.1065-0.7808-0.4510.36570.0719-0.14420.7687-0.01850.533-31.557-15.29487.4668
724.05027.244-1.0596.51548.41772.2254-0.00340.2068-0.801-0.7712-1.6999-1.4205-1.44550.12681.32321.01640.1546-0.2110.94050.20060.892-31.166-22.326195.5856
738.99443.3487-3.32129.8013-0.01618.7244-0.2110.7024-1.3726-1.223-0.22250.34720.3249-0.39640.190.40290.1343-0.11240.4068-0.10920.4233-27.1663-14.069387.9036
742.57884.3297-4.84951.9934-8.28864.12860.5552.39320.0646-1.47940.474-0.46-0.2089-0.9838-0.7260.63170.33360.0730.9571-0.17640.2363-21.5125-8.624878.6825
753.24732.1356-7.34643.71921.695.61560.13040.7143-0.1568-1.46670.7317-1.0523-0.54780.6937-0.75370.54350.15660.13380.9693-0.08450.3003-18.3629-1.835882.3349
765.5708-0.02714.84422.78449.01628.29870.24731.7118-0.0201-0.67560.3061-0.1274-1.2069-0.0552-0.39120.4693-0.1210.12360.8811-0.00640.3492-13.82715.617587.3072
774.4017-0.9982.13554.77077.83576.9394-0.84021.14140.31210.69170.8762-0.796-0.72281.7262-0.16820.7488-0.29940.28070.5430.02230.4095-9.167412.524793.6262
78-0.1723-1.2094-1.46082.0863-6.86986.5964-0.67890.3814-0.8404-2.14190.2763-1.60451.13850.56340.36410.4764-0.02060.23330.3006-0.10440.8889-1.58897.011398.4776
794.8594-5.5737-4.19522.15561.34992.05760.8147-0.1245-0.2268-0.54870.1147-1.95940.220.6879-0.87680.42140.0098-0.01420.4192-0.04280.8687-6.56381.6907103.1902
80-0.4007-6.36042.21979.0574-5.30715.1634-0.0341-1.0358-0.9360.50240.881-0.07821.08941.0169-0.76960.38130.0974-0.02770.31250.03360.6077-12.8561-4.6362106.4337
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 2:7
2X-RAY DIFFRACTION2chain A and resid 8:15
3X-RAY DIFFRACTION3chain A and resid 16:25
4X-RAY DIFFRACTION4chain A and resid 26:30
5X-RAY DIFFRACTION5chain A and resid 31:36
6X-RAY DIFFRACTION6chain A and resid 37:41
7X-RAY DIFFRACTION7chain A and resid 42:47
8X-RAY DIFFRACTION8chain A and resid 48:53
9X-RAY DIFFRACTION9chain A and resid 54:59
10X-RAY DIFFRACTION10chain A and resid 60:66
11X-RAY DIFFRACTION11chain A and resid 67:73
12X-RAY DIFFRACTION12chain A and resid 74:80
13X-RAY DIFFRACTION13chain A and resid 81:84
14X-RAY DIFFRACTION14chain A and resid 96:102
15X-RAY DIFFRACTION15chain A and resid 103:110
16X-RAY DIFFRACTION16chain A and resid 111:118
17X-RAY DIFFRACTION17chain A and resid 119:122
18X-RAY DIFFRACTION18chain A and resid 123:128
19X-RAY DIFFRACTION19chain A and resid 129:133
20X-RAY DIFFRACTION20chain A and resid 134:142
21X-RAY DIFFRACTION21chain B and resid 4:9
22X-RAY DIFFRACTION22chain B and resid 10:22
23X-RAY DIFFRACTION23chain B and resid 23:30
24X-RAY DIFFRACTION24chain B and resid 31:44
25X-RAY DIFFRACTION25chain B and resid 45:50
26X-RAY DIFFRACTION26chain B and resid 51:56
27X-RAY DIFFRACTION27chain B and resid 57:65
28X-RAY DIFFRACTION28chain B and resid 66:72
29X-RAY DIFFRACTION29chain B and resid 73:77
30X-RAY DIFFRACTION30chain B and resid 78:84
31X-RAY DIFFRACTION31chain B and resid 85:91
32X-RAY DIFFRACTION32chain B and resid 92:96
33X-RAY DIFFRACTION33chain B and resid 97:103
34X-RAY DIFFRACTION34chain B and resid 104:108
35X-RAY DIFFRACTION35chain B and resid 109:118
36X-RAY DIFFRACTION36chain B and resid 119:122
37X-RAY DIFFRACTION37chain B and resid 123:129
38X-RAY DIFFRACTION38chain B and resid 130:134
39X-RAY DIFFRACTION39chain B and resid 135:140
40X-RAY DIFFRACTION40chain B and resid 141:2001
41X-RAY DIFFRACTION41chain C and resid 4:9
42X-RAY DIFFRACTION42chain C and resid 10:16
43X-RAY DIFFRACTION43chain C and resid 17:22
44X-RAY DIFFRACTION44chain C and resid 23:28
45X-RAY DIFFRACTION45chain C and resid 29:38
46X-RAY DIFFRACTION46chain C and resid 39:48
47X-RAY DIFFRACTION47chain C and resid 49:54
48X-RAY DIFFRACTION48chain C and resid 55:60
49X-RAY DIFFRACTION49chain C and resid 61:67
50X-RAY DIFFRACTION50chain C and resid 68:74
51X-RAY DIFFRACTION51chain C and resid 75:79
52X-RAY DIFFRACTION52chain C and resid 80:85
53X-RAY DIFFRACTION53chain C and resid 86:94
54X-RAY DIFFRACTION54chain C and resid 95:100
55X-RAY DIFFRACTION55chain C and resid 101:105
56X-RAY DIFFRACTION56chain C and resid 106:109
57X-RAY DIFFRACTION57chain C and resid 110:118
58X-RAY DIFFRACTION58chain C and resid 119:122
59X-RAY DIFFRACTION59chain C and resid 123:131
60X-RAY DIFFRACTION60chain C and resid 132:143
61X-RAY DIFFRACTION61chain D and resid 4:13
62X-RAY DIFFRACTION62chain D and resid 14:27
63X-RAY DIFFRACTION63chain D and resid 28:36
64X-RAY DIFFRACTION64chain D and resid 37:41
65X-RAY DIFFRACTION65chain D and resid 42:48
66X-RAY DIFFRACTION66chain D and resid 49:54
67X-RAY DIFFRACTION67chain D and resid 55:60
68X-RAY DIFFRACTION68chain D and resid 61:66
69X-RAY DIFFRACTION69chain D and resid 67:74
70X-RAY DIFFRACTION70chain D and resid 75:81
71X-RAY DIFFRACTION71chain D and resid 82:86
72X-RAY DIFFRACTION72chain D and resid 87:93
73X-RAY DIFFRACTION73chain D and resid 94:99
74X-RAY DIFFRACTION74chain D and resid 100:104
75X-RAY DIFFRACTION75chain D and resid 105:109
76X-RAY DIFFRACTION76chain D and resid 110:118
77X-RAY DIFFRACTION77chain D and resid 119:122
78X-RAY DIFFRACTION78chain D and resid 123:130
79X-RAY DIFFRACTION79chain D and resid 131:135
80X-RAY DIFFRACTION80chain D and resid 136:143

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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