[日本語] English
- PDB-7rgt: The crystal structure of RocC, containing FinO domain, 1-126 -

+
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: 7rgt
タイトルThe crystal structure of RocC, containing FinO domain, 1-126
要素Repressor of competence, RNA Chaperone
キーワードRNA BINDING PROTEIN / RNA chaperone / FinO / ProQ
機能・相同性RNA strand-exchange activity / RNA chaperone ProQ / ProQ/FinO domain superfamily / ProQ/FINO family / ProQ/FinO domain / ProQ/FINO family / RNA strand annealing activity / post-transcriptional regulation of gene expression / ProP effector
機能・相同性情報
生物種Legionella pneumophila (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.02 Å
データ登録者Kim, H.J. / Edwards, R.A. / Glover, J.N.M.
資金援助 カナダ, 1件
組織認可番号
Natural Sciences and Engineering Research Council (NSERC, Canada) カナダ
引用ジャーナル: Nat Commun / : 2022
タイトル: Structural basis for recognition of transcriptional terminator structures by ProQ/FinO domain RNA chaperones.
著者: Kim, H.J. / Black, M. / Edwards, R.A. / Peillard-Fiorente, F. / Panigrahi, R. / Klingler, D. / Eidelpes, R. / Zeindl, R. / Peng, S. / Su, J. / Omar, A.R. / MacMillan, A.M. / Kreutz, C. / ...著者: Kim, H.J. / Black, M. / Edwards, R.A. / Peillard-Fiorente, F. / Panigrahi, R. / Klingler, D. / Eidelpes, R. / Zeindl, R. / Peng, S. / Su, J. / Omar, A.R. / MacMillan, A.M. / Kreutz, C. / Tollinger, M. / Charpentier, X. / Attaiech, L. / Glover, J.N.M.
履歴
登録2021年7月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年11月9日Provider: repository / タイプ: Initial release
改定 1.12022年11月30日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22024年4月3日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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: Repressor of competence, RNA Chaperone
B: Repressor of competence, RNA Chaperone
C: Repressor of competence, RNA Chaperone
D: Repressor of competence, RNA Chaperone
E: Repressor of competence, RNA Chaperone
F: Repressor of competence, RNA Chaperone
G: Repressor of competence, RNA Chaperone
H: Repressor of competence, RNA Chaperone
I: Repressor of competence, RNA Chaperone
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)133,91318
ポリマ-133,0499
非ポリマー8659
8,701483
1
A: Repressor of competence, RNA Chaperone
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)14,8792
ポリマ-14,7831
非ポリマー961
181
タイプ名称対称操作
identity operation1_555x,y,z1
2
B: Repressor of competence, RNA Chaperone
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)14,8792
ポリマ-14,7831
非ポリマー961
181
タイプ名称対称操作
identity operation1_555x,y,z1
3
C: Repressor of competence, RNA Chaperone
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)14,8792
ポリマ-14,7831
非ポリマー961
181
タイプ名称対称操作
identity operation1_555x,y,z1
4
D: Repressor of competence, RNA Chaperone
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)14,9753
ポリマ-14,7831
非ポリマー1922
181
タイプ名称対称操作
identity operation1_555x,y,z1
5
E: Repressor of competence, RNA Chaperone
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)14,8792
ポリマ-14,7831
非ポリマー961
181
タイプ名称対称操作
identity operation1_555x,y,z1
6
F: Repressor of competence, RNA Chaperone
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)14,8792
ポリマ-14,7831
非ポリマー961
181
タイプ名称対称操作
identity operation1_555x,y,z1
7
G: Repressor of competence, RNA Chaperone
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)14,8792
ポリマ-14,7831
非ポリマー961
181
タイプ名称対称操作
identity operation1_555x,y,z1
8
H: Repressor of competence, RNA Chaperone


分子量 (理論値)分子数
合計 (水以外)14,7831
ポリマ-14,7831
非ポリマー00
181
タイプ名称対称操作
identity operation1_555x,y,z1
9
I: Repressor of competence, RNA Chaperone
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)14,8792
ポリマ-14,7831
非ポリマー961
181
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)139.010, 100.303, 110.718
Angle α, β, γ (deg.)90.000, 107.571, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))
d_2ens_1(chain "B" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))
d_3ens_1(chain "C" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))
d_4ens_1(chain "D" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))
d_5ens_1(chain "E" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))
d_6ens_1(chain "F" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))
d_7ens_1(chain "G" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))
d_8ens_1(chain "H" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))
d_9ens_1(chain "I" and (resid 28 through 71 or resid 73 through 114 or resid 116 or resid 118 through 122))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALALYSA10 - 53
d_12ens_1LYSGLUA55 - 96
d_13ens_1ALAALAA98
d_14ens_1METLYSA100 - 104
d_21ens_1ALALYSB21 - 64
d_22ens_1LYSGLUB67 - 108
d_23ens_1ALAALAB111
d_24ens_1METLYSB113 - 117
d_31ens_1ALALYSC7 - 50
d_32ens_1LYSGLUC53 - 94
d_33ens_1ALAALAC96
d_34ens_1METLYSC98 - 102
d_41ens_1ALALYSD11 - 54
d_42ens_1LYSGLUD57 - 98
d_43ens_1ALAALAD100
d_44ens_1METLYSD102 - 106
d_51ens_1ALALYSE7 - 50
d_52ens_1LYSGLUE53 - 94
d_53ens_1ALAALAE96
d_54ens_1METLYSE98 - 102
d_61ens_1ALALYSF5 - 48
d_62ens_1LYSGLUF51 - 92
d_63ens_1ALAALAF94
d_64ens_1METLYSF96 - 100
d_71ens_1ALALYSG26 - 69
d_72ens_1LYSGLUG73 - 114
d_73ens_1ALAALAG116
d_74ens_1METLYSG118 - 122
d_81ens_1ALALYSH7 - 50
d_82ens_1LYSGLUH52 - 93
d_83ens_1ALAALAH95
d_84ens_1METLYSH98 - 102
d_91ens_1ALALYSI1 - 44
d_92ens_1LYSGLUI47 - 88
d_93ens_1ALAALAI90
d_94ens_1METLYSI92 - 96

NCS oper:
IDCodeMatrixベクター
1given(0.55948425896, 0.616819570711, -0.55363433886), (0.712209648999, -0.016114216141, 0.701781837832), (0.423951388545, -0.786939609644, -0.448320500228)18.5674097639, -0.588157672659, 35.4002971137
2given(-0.475171235363, 0.696522186676, -0.537651504742), (-0.71269802424, 0.0536774158972, 0.699414227241), (0.516017270378, 0.715524687548, 0.47090402226)10.6070156707, 37.0548152496, 27.1444725543
3given(0.49101794146, -0.715110037319, -0.497512829673), (-0.720454152401, -0.0122828779322, -0.693393787972), (0.489741968237, 0.698903974402, -0.521235109248)17.9684425401, 74.4317752421, 36.68368628
4given(0.509396006244, 0.73360177018, 0.449826801792), (0.682289208203, -0.0257622009707, -0.730628322317), (-0.524401702125, 0.67909112186, -0.513651733199)-24.7760840762, 13.2338230526, 27.9419508606
5given(0.544733608578, 0.761622287806, 0.350993997673), (0.641341079318, -0.108680071182, -0.759519757549), (-0.540321122727, 0.638842807617, -0.54766134745)8.85954540085, 38.297556593, 27.5292349351
6given(-0.0652114797726, -0.118097898805, -0.990858390086), (-0.12614529462, -0.984030233449, 0.125586083243), (-0.989866065461, 0.133181777872, 0.0492725734253)54.4430617645, -1.29986104266, 51.1746409709
7given(-0.11926769294, -0.128492040602, -0.984512576315), (0.16284329228, -0.980693885297, 0.10826617893), (-0.979416805849, -0.147408611833, 0.137889164103)56.8163926248, 15.9592823408, 85.5488394714
8given(0.34406593401, 0.729877812635, -0.590675047447), (0.792069894405, 0.112207624864, 0.600028942052), (0.504226055883, -0.674305440839, -0.539507420731)-10.4196958027, -25.7076068328, 34.6440023093

-
要素

#1: タンパク質
Repressor of competence, RNA Chaperone


分子量: 14783.208 Da / 分子数: 9 / 断片: ProQ/FinO-domain, UNP residues 1-126 / 由来タイプ: 組換発現
由来: (組換発現) Legionella pneumophila (バクテリア)
遺伝子: C3926_00530, DIZ73_10055 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A128QHZ1
#2: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 9 / 由来タイプ: 合成 / : SO4
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 483 / 由来タイプ: 天然 / : H2O
研究の焦点であるリガンドがあるかN

-
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: 2.77 Å3/Da / 溶媒含有率: 55.52 %
結晶化温度: 289.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.3
詳細: 0.2M Ammonium Sulfate, 0.1M HEPES:NaOH, pH 7.3, 20% PEG 3350 with various additives

-
データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: CLSI / ビームライン: 08ID-1 / 波長: 1.03319 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2019年1月29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: 1.03319 Å / 相対比: 1
反射解像度: 2.02→50 Å / Num. obs: 94465 / % possible obs: 99.7 % / 冗長度: 6.2 % / Biso Wilson estimate: 44.09 Å2 / CC1/2: 0.989 / Net I/σ(I): 17.4
反射 シェル解像度: 2.02→2.05 Å / 冗長度: 4.7 % / Num. unique obs: 4477 / CC1/2: 0.672 / % possible all: 95.6

-
解析

ソフトウェア
名称バージョン分類
MxDCデータ収集
HKL-2000データスケーリング
Cootモデル構築
HKL-2000data processing
PHASER位相決定
PHENIX1.18.2_3874精密化
精密化構造決定の手法: 分子置換
開始モデル: RocC(24-126)

解像度: 2.02→45.3 Å / SU ML: 0.2254 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 24.2696
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2126 4642 4.92 %
Rwork0.1928 89766 -
obs0.1938 94408 99.48 %
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
原子変位パラメータBiso mean: 66.76 Å2
精密化ステップサイクル: LAST / 解像度: 2.02→45.3 Å
タンパク質核酸リガンド溶媒全体
原子数7607 0 45 483 8135
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.0057806
X-RAY DIFFRACTIONf_angle_d0.707510492
X-RAY DIFFRACTIONf_chiral_restr0.04741190
X-RAY DIFFRACTIONf_plane_restr0.00471350
X-RAY DIFFRACTIONf_dihedral_angle_d13.98063050
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.681712718795
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.575110915192
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.720679609991
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.812835330516
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.652418941187
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.874465057229
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.921404550833
ens_1d_9AX-RAY DIFFRACTIONTorsion NCS0.989480621714
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.040.29871580.29062727X-RAY DIFFRACTION90.58
2.04-2.070.31381620.28762862X-RAY DIFFRACTION97.05
2.07-2.090.31081470.26782969X-RAY DIFFRACTION98.58
2.09-2.120.27661580.25032902X-RAY DIFFRACTION99.42
2.12-2.150.25091530.24953047X-RAY DIFFRACTION99.84
2.15-2.180.30621430.24012977X-RAY DIFFRACTION99.84
2.18-2.210.27551410.22223016X-RAY DIFFRACTION100
2.21-2.240.24771590.22092997X-RAY DIFFRACTION99.97
2.24-2.270.29991790.21752977X-RAY DIFFRACTION99.94
2.28-2.310.26461330.21583029X-RAY DIFFRACTION99.97
2.31-2.350.24031610.22082963X-RAY DIFFRACTION99.9
2.35-2.390.25711620.21533018X-RAY DIFFRACTION100
2.39-2.440.23191460.21033009X-RAY DIFFRACTION99.97
2.44-2.490.25241590.20772985X-RAY DIFFRACTION100
2.49-2.540.23931640.21062978X-RAY DIFFRACTION99.97
2.54-2.60.23561410.20823019X-RAY DIFFRACTION99.97
2.6-2.670.24391570.21313015X-RAY DIFFRACTION100
2.67-2.740.27161520.22352957X-RAY DIFFRACTION99.97
2.74-2.820.28831610.22453018X-RAY DIFFRACTION99.97
2.82-2.910.26151740.23672992X-RAY DIFFRACTION100
2.91-3.020.2891370.23223030X-RAY DIFFRACTION99.97
3.02-3.140.24261420.22133036X-RAY DIFFRACTION100
3.14-3.280.2751330.21673023X-RAY DIFFRACTION100
3.28-3.450.2041370.19553040X-RAY DIFFRACTION99.97
3.45-3.670.1861510.18322995X-RAY DIFFRACTION100
3.67-3.950.17311800.16063010X-RAY DIFFRACTION100
3.95-4.350.18191610.16033016X-RAY DIFFRACTION100
4.35-4.980.15511570.15273055X-RAY DIFFRACTION100
4.98-6.270.18221700.17963010X-RAY DIFFRACTION100
6.27-45.30.18561640.16973094X-RAY DIFFRACTION99.66
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)
17.51986316165-0.0194132529103-2.767784275638.27009176812-0.5666592696052.740169154670.1605042079940.297760872345-0.692986081268-0.204463402632-0.2629462059710.7131402702041.17332180962-0.1722611837880.03029183721640.8371791962850.152166696637-0.04963990888540.652794287177-0.1398004234280.48426989918925.1065334623-4.554013775398.85706867662
23.20893811193-0.820126993878-0.8773948228795.335315503983.687638227246.049719789770.3927448651030.546783975468-0.13148239009-0.778243193151-0.199119925817-0.4089136812320.0419480997310.0726077611153-0.2180096983460.3950839220810.1163797969030.02453256099580.354696793869-0.03766431128870.34130758660827.06094039657.7799570376410.674028816
35.51087489558-1.05531289443-1.924259830576.732280073374.162212828462.916188921380.3832188505980.83706568714-0.372645008839-0.604756401134-0.4939332766110.4182563969450.6930379927590.1075211534810.1810005838130.3925529793870.118839288061-0.05582652163970.379383224374-0.1220008218930.34478104499319.66483267140.99373564490510.9685386009
48.365934857845.291717117610.3640868999596.90441590346-3.16972910864.96282188470.1811071789130.0763422650169-0.776209002810.0151992565919-0.321104856773-0.5570700465190.5534521427490.7154178101370.208799347560.4395759900610.0770141518776-0.02936867171770.36101108752-0.05779545923990.39987123162423.7666926543.8265587929225.2957894044
58.60101084067-1.24414088561-3.114375636082.929445668724.406034391688.013848341080.3933138079720.2470663990710.237576456475-0.432751094716-0.132301108626-0.46759484766-0.4862162081570.0368423870304-0.2812253302830.3701145484630.03115597361930.02882570598050.256875261179-0.002152049940780.30636040703926.189463478716.478219798121.5111238579
65.978243179820.299101712585-0.5712550833713.49086027161-2.953528490892.53901270089-0.188727010533-0.323673878118-0.6352768393181.01232904390.4670294061782.02279179081-0.0963610259984-0.871952285971-0.231034473290.477023206496-0.07668557738930.0813501700870.5734690641120.01209810873070.62667776052114.84862776946.5390457997130.4218252366
79.09500542622-3.233782999740.9248259308437.79490056423-4.364927801176.4612055068-1.22862018374-0.107733250798-0.5135116095371.266976737361.121984719240.616468793164-0.266749084233-1.757642208030.01408325278571.08521606341-0.0366253896210.1497341264591.09474866941-0.310327374381.01958728033-12.189807268816.391962864745.3286093652
87.03173424914-1.541492021252.614342047275.887803315250.414811218779.378768743610.0742686367481-1.02949836578-0.2982227026230.783537461311-0.1046147465040.8538089826570.140026763302-0.7812367838160.06026217438480.693080538383-0.04383241146740.08740823245740.3841664489810.01946597447370.43894069676824.346781690723.426654360445.8613308788
98.328787657111.041526229021.905609068946.42120385321-0.5803600264767.275931373210.134455969392-0.7268497361080.712641992310.415437169133-0.06976170405260.0289680719189-1.390001996070.164053246952-0.08776776942390.478045919017-0.08051020938930.07474435196070.344293817670.002223657475010.41294384541130.700483943533.027132160833.7965926118
108.46194267245-0.02275103058491.886712754464.0673975173-3.905544771674.766759947750.177772597601-0.0523814136382-0.5491831809570.267164897938-0.233618403534-0.563258550851.245878946931.071310512090.1104724628720.5486090829110.0664316815607-0.01275628031750.3614270650650.01701825152520.42011039867834.90100321418.113535422138.5162637353
113.14893742563-1.17406397471.667373583953.63071474144-0.4405100536214.218361878140.1585780132230.09163213627140.1729630165360.0281918336483-0.1340730978380.04973112205270.001952760712910.141661160764-0.02825871277430.296724045095-0.01514129493420.06435562317450.215534429576-0.008887594647510.28372795044526.637006847128.443260528130.6125998781
124.09963492285-2.2621598696-3.992318765752.430364751022.284435783174.350174429770.3499734387140.778839407769-0.29550556469-0.960731355052-0.3374328635481.262019467030.322478804347-1.15022804765-0.03165939884680.495115012265-0.0293322618179-0.1104112088180.4758349594610.0288235632790.62442865027215.269046675730.598658521622.1507994494
134.121845004721.17640323321-0.8332944233183.098128184310.5226915353557.49243704887-0.06489181658020.756572085629-0.205517121034-0.407641569061-0.336047960550.4269414613930.177441463165-1.498641150330.2855031707750.405343866072-0.1225640359820.03278928217540.703071475958-0.2028087666870.465395961402-8.2790349956124.015065131946.5027930734
147.761747870083.629593488460.2988243543948.03646574069-0.5945374380315.071444026510.2846163217810.00219082132814-0.4336027794020.473183641329-0.1255970687791.048814678380.171419215552-1.04386000161-0.1130675205610.404624543863-0.09510548457920.06161213120340.63476512386-0.08649453396520.567750510251-8.0276721896430.319396290657.6066635942
158.612483929265.965017077316.710905372726.077481268577.488690453449.36435360370.3983582893830.30906681362-1.080860039070.2420649373940.274865815841-1.711542717860.636135953903-0.260937142501-0.595413839750.460669044138-0.1005675660610.05156731525880.591723691168-0.1329153020440.5330004151113.0464560772822.538328924745.9927823596
165.24908606556-3.7217318433-4.294876060727.648534794196.906510921429.268891863760.1502416460060.622636148542-0.21413448366-0.68186898325-0.465342033790.240736977995-0.669213614479-0.653379409610.2918824817070.413627978085-0.08102667499170.006665513547080.646912494352-0.1109988261160.370527269693-3.8753231599630.726315279742.9203115078
179.119665371-5.665021181866.426431164129.64462570854-7.54745011418.16977255697-0.4892572079020.573833005508-0.964451233202-0.1724785652770.6742734796510.25099611490.368777778023-1.09277377132-0.1333872859710.419513622313-0.1440921264540.05036949368070.621458677039-0.08781276589330.350875765113-11.646734770638.192297703654.0964970003
183.67524847995-0.873207628631-0.008565906806657.125948509131.137645996155.814265320740.0113159586941-0.3163776212130.02520540086820.4353708483220.250397375582-0.1342509056770.199895253563-0.188978941347-0.2387032007040.353012791086-0.1091871698470.02459885368430.417700774756-0.07698203955640.351667624507-1.9181219414934.164982206762.5238385195
194.24578812776-4.007573821724.938415239997.7701211379-4.222163245085.696918525950.5561238078980.3828412708761.11256084408-0.0921351189978-0.37369229732-0.429104542223-0.8235572158240.4486603093440.1257235664530.720728796029-0.007903343134740.2477348084630.5971881814930.0127012384440.603892447083-6.9398121843847.832137375454.5570889818
207.18904040568-3.347688920531.520770247993.67445341741-3.241760804498.446962418390.4857736185710.2419054232751.11621759603-1.6684560874-0.493647211714-0.561080447115-0.9073101393282.17320332339-0.05961862392680.775954279979-0.2731212821370.1828078997890.721394923088-0.1668169470991.0187756521729.54789954750.414757490140.399371775
217.962749869450.9209531234420.1741409587914.38742005232-1.266617729747.579762820520.0991956457381-0.587095793388-0.610385141767-0.1042859129860.292071646879-0.9647455609290.09463525628130.772265266949-0.4488658980670.354346273525-0.03667704218310.03627575749240.369835473979-0.09811123318790.55421292534518.024041148840.528867454847.8920242841
226.769707403821.74068287827-0.3102797358351.33722558696-1.330045311621.778300377130.0729295429272-0.7396222749951.344585158660.7543780997870.497176584205-1.3632328977-1.149319162730.957288809813-0.3705412108350.603681733346-0.127027430751-0.02731243430970.62368813693-0.3421887234811.1071522913922.919182467155.286099098452.0344804484
237.803345955176.58076053391.367384811996.372154709170.4285324099760.6938918536310.06781301640810.5887719093381.00016214358-1.802593618760.500545006695-1.42277188989-1.286404675230.835581991396-0.2094542088140.592380051343-0.2143832446060.2337012077510.423936891725-0.1185464108790.94704909838921.661858164152.920220947741.2746255248
249.687718464950.453177935041-2.847523596695.361952798461.219709197528.22553656703-0.047294643866-0.06388855436030.251738090566-0.858607052737-0.0449121522473-0.9612685087930.5325948159780.5406853341230.1082701319640.379799272380.02140614143920.1293714778070.299013107655-0.01204899197640.44355396443714.360593771539.785635322237.7464746101
259.453979306512.471273911761.114081623866.34504707816-1.045837058673.176185567890.0367876947821-0.5677870254690.0836056858133-0.000460418824141-0.0415492206467-0.2951016560460.0819368626852-0.21716162560.009764171727840.335660853194-0.001228056700780.01433611656870.403669446472-0.1092890636050.3696872361118.4453176989740.505774565449.7880468859
264.09712238333-4.50422181755-0.4081737377147.935663154233.209009328834.959218069390.8605255722431.167835857180.612679731231-1.52101506525-0.877377196983-0.0365885692388-1.9502182832-1.614324331460.03551619911730.831352794830.128445618737-0.09192768237280.5976363575910.01720442106330.5053824673035.2676771445442.670962914432.7131845722
271.31116523029-2.3408718537-1.209101498187.07783623914-0.9190287234525.95489288093-0.571192667364-0.9675299845761.21930599514-0.501085318751-0.2955711761711.06907359668-1.00992490623-1.814401828460.8544438754170.8601110482720.515255123493-0.1795492910131.04716212439-0.003548570015950.859059137978-9.5033748085224.73257660127.53143374395
287.42994155568-1.646459910890.7278953249886.57333008134-2.210553506953.186753720650.0918060650820.4312040674440.758725918222-0.146036409993-0.1374615111220.729002019203-1.18677404822-1.18137578890.02487767322760.5870169744540.279204778665-0.118199244770.701288268904-0.04390915602770.511940639138-3.4048651579321.994740486913.2567701865
296.236995256280.1189171136380.9884392986123.360330977940.7629249976176.1046110405-0.1169416537410.4856496597140.339284024771-0.1311880902270.01597569148270.263576945023-0.334002137553-0.2882115977180.1007207093680.3726510365410.0738309297381-0.0615910056190.3231145025510.0003626706540250.2547149004967.7319059033513.817318536211.6922834641
305.235474124835.51778429175.524562932528.094668657465.010277100116.009149022450.244746896573-0.295364543784-0.819543659330.17569467146-0.006273008529780.5369476718471.44718153221-1.29316172068-0.3512570650120.634219829211-0.140734880428-0.0009980250346950.695474141305-0.04095955547440.6328568247311.295910436440.8806820795369.19614144339
314.214243363691.23538800865-1.609018650125.11585338542-1.337495341258.241963925560.02659729622140.01146228248150.4458754424580.2171285418130.1675050045530.689680874949-1.11284942901-0.0656431180997-0.1747867944580.7270834059570.006178627195530.09645649466140.4443478803880.1689193903360.53798769999231.45574931847.384578526810.7262618359
325.9676712213-1.26501108682-1.58541916488.816182867570.3440201854945.4806652815-0.02107022089940.7570354847460.0848119478844-0.7562071735630.04352934095220.6587442922890.12250482294-0.942192974014-0.1448784208250.692360199806-0.01022766620320.05887580947340.6001996211170.1953830489720.57336025951627.020833149239.76835251119.15676257375
337.238929111361.790743853730.4630909364387.02169462241-1.0320829536.74673682497-0.379538841640.120593277681-1.19752085486-0.110225562667-0.0951581346714-0.6232388389261.66839010551.06101565790.4220180786251.021343676480.09373447299050.2724613464480.6264605628960.184369984410.57281195080339.455021711631.612167717610.6593143439
345.53881733984-3.64422018545-5.291136611288.29753293343.640571806975.158249922290.559690023198-0.3929463149231.736493222251.14343581817-0.164068693418-0.15188239306-0.9103132852011.13590341837-0.4728242825980.985461822917-0.0711818677647-0.0882343685040.69964938371-0.06949864748480.85019598272632.255051749129.474632945850.7424019812
358.165417735492.911675798130.301169219675.557581444982.220820733142.52135901229-0.07394207622950.04446102681661.49659828973-0.778208260916-0.498641852227-0.461139288501-0.9438239165250.8481717061470.5783848458040.6836340367880.000832549307754-0.05277765914820.8062474667420.2387304936160.8339005516245.28802028913.1636347929526.5410046367
366.318185699830.830679345396-0.9575457789018.43602372879-0.7913964192685.21888065887-0.06056956768740.3149313154650.0976583131663-0.798976692871-0.28220511716-0.7951504039810.5143948035781.076317232510.29735292760.4946532926390.1397444091310.03264702190660.5934397349470.1254651306730.38715627978241.7231651344-8.3277560829728.2619654541
376.73473378036-3.37609112622-0.7245939188037.18681423073-1.394445790999.44603135260.1018078739730.0944754799233-1.24327416599-0.799903177559-0.03907798086840.8894910362851.26201438589-0.0944882058954-0.05550639789220.616605768784-0.0142795884195-0.1307653515110.3673048487090.039149657750.55285562452528.9410017152-14.343344522828.7917765663
383.61509679795-3.622430336631.801307200094.44189186587-4.012221269197.03835878305-0.687233083554-1.65465539179-0.5495131510571.716885334421.619968244911.01792735424-0.71589848783-1.15157643463-0.8871458859610.7306440505470.04569299678690.08604671754161.044393843690.1516509094570.64974476794222.4334621836-5.8647713974938.9619982011
395.832654512965.237408289995.950330279856.286240070564.548018666676.507066508081.05041292784-0.4007274656471.229756721670.4538052226950.758692624061-1.19923834863-1.410513323671.319454677-1.749499281131.01098285562-0.4421821884940.2224791870630.894639080986-0.1434443914751.0373783341445.063803951224.06666660161.2590036595
402.06291501967-0.3235502372910.9546081902856.85052099155-0.5471474163748.04975462494-0.205369796497-0.6812973324240.1197601214170.5021337755680.264750295783-1.12435814694-0.1365323362191.47399654442-0.01343020413770.653554888084-0.032887128837-0.1126200807570.775009175174-0.03498163016580.6329564959542.172366692513.878586843359.2696586188
417.231092899683.18753031071.771082061097.406027557611.088073937215.48560417419-0.415557063764-0.3865019772281.259972298530.5218141032140.559219864489-0.674699226855-0.5574707817281.3970093555-0.1277601494330.774391508019-0.0708710682627-0.04212545255480.958522376422-0.2430990286530.68399264012138.519874767119.075823559766.8975615188
427.685211131671.124081357870.2084705130397.239051261932.308199293717.16863269156-0.00464380200697-1.202583152230.4033543060251.00579493222-0.0745304029320.52694186211-0.286759399306-0.2530138222360.1232044851220.6405252764890.07000927275260.06285195171290.5143279310210.02931952871760.37500802740127.560492062710.31371831366.7672295742
436.111362978211.92288908338-0.2907715881314.2727735015-0.1016050220226.188342363750.47501985507-1.81493848178-1.290633065470.610807430794-0.5067012784570.4861146710821.73954151892-1.67696838027-0.5379006934221.1377144195-0.431415202671-0.08899887801980.8668123177530.1425012512390.735405571059-4.353413848453.1325734674743.8814974867
448.246325230731.633029702233.689411934062.69892264009-1.900145401977.054841513220.710475739374-0.499431089206-0.4334037887850.312101137602-0.461206395980.7393383384550.937748510543-0.679722614407-0.3028561484370.483012506181-0.2530065483960.06045003446520.53822042094-0.1457503548930.487404735261-4.555859564959.140719301434.6995897636
457.376382748760.4763145250713.187163533793.83867759715-1.60993416332.256643150171.12093065846-1.05797011417-2.68824415460.2598660324590.288754755741-0.5374749976193.21349191637-0.503563878795-0.7063065212811.59134925433-0.153894501575-0.3805914524680.7059331466730.1271477584421.347761963651.77301998406-4.2059112098240.4217130004
460.8468572336620.488503212875-0.06008654051331.112494027511.241690772871.971638836260.828241047651-0.528516196462-2.574772600110.8854502253210.2021374371871.582665377131.64178468389-0.758491450713-0.6088904978421.30601221252-1.36702675036-0.296246740080.9037577376860.1756197580281.34005703598-9.16759676665-3.8050879359537.9339277728
472.155152565521.63113693089-3.621287134755.77518042467-2.132924513556.360513984530.6886307177890.501107618782-0.07339882911340.446645030116-0.3175772617930.7654932718140.723533518551-1.65850592738-0.3302234962750.604172295702-0.268489000132-0.09696011517121.14260624271-0.1096739399080.748257041601-11.711356050210.091414895826.5437200492
486.811236387240.003024071912321.191993039976.28310697507-1.581799749415.112010630110.5074887677920.241333978947-0.427875918707-0.15220380593-0.2741766585910.09758376199431.10082467689-0.210183998762-0.2244527397360.509957231144-0.0491800657495-0.01091294912510.601466868778-0.1571217210880.5019384016340.274432305418.4838945864626.8371750358
492.7583939232.10840832222-3.278704299434.11947119354-0.9013459794135.54168800921-0.6034163857151.601500860870.563301984113-0.5834507286360.5226289222421.132415713581.40551691388-1.37736385653-0.04579672615790.953800553289-0.33462733024-0.3790194804491.49037883258-0.1869639716891.03624225746-17.14613747615.8208599690719.847317119
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 19 through 35 )AA19 - 351 - 17
22chain 'A' and (resid 36 through 67 )AA36 - 6718 - 49
33chain 'A' and (resid 68 through 83 )AA68 - 8350 - 65
44chain 'A' and (resid 84 through 90 )AA84 - 9066 - 72
55chain 'A' and (resid 91 through 109 )AA91 - 10973 - 91
66chain 'A' and (resid 110 through 125 )AA110 - 12592 - 107
77chain 'B' and (resid -2 through 17 )BB-2 - 171 - 10
88chain 'B' and (resid 18 through 35 )BB18 - 3511 - 28
99chain 'B' and (resid 36 through 52 )BB36 - 5229 - 45
1010chain 'B' and (resid 53 through 67 )BB53 - 6746 - 60
1111chain 'B' and (resid 68 through 109 )BB68 - 10961 - 103
1212chain 'B' and (resid 110 through 123 )BB110 - 123104 - 118
1313chain 'C' and (resid 22 through 40 )CC22 - 401 - 19
1414chain 'C' and (resid 41 through 52 )CC41 - 5220 - 31
1515chain 'C' and (resid 53 through 67 )CC53 - 6732 - 46
1616chain 'C' and (resid 68 through 83 )CC68 - 8347 - 63
1717chain 'C' and (resid 84 through 90 )CC84 - 9064 - 70
1818chain 'C' and (resid 91 through 109 )CC91 - 10971 - 89
1919chain 'C' and (resid 110 through 123 )CC110 - 12390 - 103
2020chain 'D' and (resid 18 through 35 )DD18 - 351 - 18
2121chain 'D' and (resid 36 through 52 )DD36 - 5219 - 35
2222chain 'D' and (resid 53 through 67 )DD53 - 6736 - 50
2323chain 'D' and (resid 68 through 83 )DD68 - 8351 - 67
2424chain 'D' and (resid 84 through 90 )DD84 - 9068 - 74
2525chain 'D' and (resid 91 through 109 )DD91 - 10975 - 93
2626chain 'D' and (resid 110 through 125 )DD110 - 12594 - 109
2727chain 'E' and (resid 22 through 35 )EE22 - 351 - 14
2828chain 'E' and (resid 36 through 83 )EE36 - 8315 - 63
2929chain 'E' and (resid 84 through 109 )EE84 - 10964 - 89
3030chain 'E' and (resid 110 through 125 )EE110 - 12590 - 105
3131chain 'F' and (resid 24 through 67 )FF24 - 671 - 44
3232chain 'F' and (resid 68 through 90 )FF68 - 9045 - 68
3333chain 'F' and (resid 91 through 122 )FF91 - 12269 - 100
3434chain 'G' and (resid -3 through 15 )GG-3 - 151 - 13
3535chain 'G' and (resid 16 through 35 )GG16 - 3514 - 33
3636chain 'G' and (resid 36 through 83 )GG36 - 8334 - 83
3737chain 'G' and (resid 84 through 109 )GG84 - 10984 - 109
3838chain 'G' and (resid 110 through 125 )GG110 - 125110 - 125
3939chain 'H' and (resid 22 through 35 )HH22 - 351 - 14
4040chain 'H' and (resid 36 through 67 )HH36 - 6715 - 46
4141chain 'H' and (resid 68 through 90 )HH68 - 9047 - 69
4242chain 'H' and (resid 91 through 124 )HH91 - 12470 - 104
4343chain 'I' and (resid 28 through 35 )II28 - 351 - 8
4444chain 'I' and (resid 36 through 52 )II36 - 529 - 25
4545chain 'I' and (resid 53 through 67 )II53 - 6726 - 40
4646chain 'I' and (resid 68 through 83 )II68 - 8341 - 57
4747chain 'I' and (resid 84 through 95 )II84 - 9558 - 69
4848chain 'I' and (resid 96 through 109 )II96 - 10970 - 83
4949chain 'I' and (resid 110 through 122 )II110 - 12284 - 96

+
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