SAXSdb — 9i1j

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9i1j
沉积日期 deposition_date	2025-01-16
最后修订 last_revision	2025-12-10
结构标题 title	Cryo-EM structure of mouse RNF213:UBE2L3 transthiolation intermediate, chemically stabilized, and ATPgS
关键词 keywords	E3 ligase, ubiquitin, AAA ATPase, LIGASE; LIGASE
实验方法 method	ELECTRON MICROSCOPY

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	70.68 Å
回转半径 Rg (电子) rg_electron	71.07 Å
零角强度 I(0) i0	3737970000.00
分子量 molecular_weight	523500.0 kDa
排除体积 excluded_volume	658200 Å³
包络体积 envelope_volume	1004000 Å³
水化壳体积 shell_volume	122360 Å³
包络直径 envelope_diameter	237.3 Å
壳层 Rg shell_rg	64.70 Å
包络 Rg envelope_rg	69.90 Å
形状 Rg shape_rg	71.06 Å
总 Rg total_rg	70.99 Å
总原子数 total_atoms	36793
残基数 n_residues	4576
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	210.3 Å
Rg (实空间) rg_real	70.78 Å
Rg 误差 (实空间) rg_real_error	1.21 Å
I(0) (实空间) i0_real	3.7320e+09
I(0) 误差 (实空间) i0_real_error	7.2670e+07
Rg (倒空间) rg_reciprocal	69.33 Å
I(0) (倒空间) i0_reciprocal	3726000000.0000
解质量估计 total_estimate	0.8344
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	66.9 Å
偏度 Skewness skewness	0.471
峰度 Kurtosis kurtosis	-0.529
角度范围 angular_range	— – 0.1100 Å⁻¹
当前正则化参数 α current_alpha	0.0120
最高正则化参数 α highest_alpha	203200000.0000
实空间数据点数 n_real_points	23
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.020

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (6)

Entity 1 polymer

描述 description	E3 ubiquitin-protein ligase RNF213
分子量 formula_weight	552623.4 kDa
EC 编号 ec_number	2.3.2.27,3.6.4.-
突变 mutation	delta N300
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	36793

MASWSHPQFEKGSTSAFNPRDTVTVYFHAIVSRHFGFNPEEHKVYVRGGEGLGQKGWTDACEMYCTQDLHDLGSLVEGKMDIPRQSLDKPIPYKYVIHRGGSSKDTVEYEFIYEQAQKKGEHVNRCLRVVSTSLGNGDWHQYDDIICMRSTGFFQQAKNRILDSTRKELLKGKKQAAVVMLDRIFSVLQPWSDINLQSFMTQFLQFYSVVREPMIHDGRARKWTSLQYEEKEVWTNLWEHVKKQMAPFLEGKSGESLPADCPVRSKLTLGLSILFMVEAAEFTVPKKDLDSLCYLLIPSAGSPEALHSDLSPVLRIRQRWRIYLTNLCLRCIDERCDRWLGILPLLHTCMQKSPPKKNSKSQPEDTWAGLEGISFSEFRDKAPTRSQPLQFMQSKMALLRVDEYLFRSWLSVVPLESLSSYLENSIDYLSDVPVRVLDCLQGISYRLPGLRKISNQNMKKDVENVFKMLMHLVDIYQHRIFGENLLQIYLTECLTLHETVCNITANHQFFEIPALSAELICKLLELSPPGHTDEGLPEKSYEDLVTSTLQEALATTRNWLRSLFKSRMLSISSAYVRLTYSEEMAVWRRLVEIGFPEKHGWKGSLLGDMEGRLKQEPPRLQISFFCSSQCRDGGLHDSVSRSFEKCVIEAVSSACQSQTSVLEGLSCQDLQKFGTLLSAVITKSWPVHNGEPVFDVDEIFKYLLKWPDVRQLFELCGTNEKIIDNITEEGRQLMATAESVFQKVAGELENGTIVVGQLELILEHQSQFLDIWNLNRRRLPSQEKACDVRSLLKRRRDDLLFLKQEKRYVESLLRQLGRVKHLVQVDFGNIEIIHSQDLSNKKLNEAVIKLPNSSSYKRETHYCLSPDIREMASKLDSLKDSHIFQDFWQETAESLNTLDKDPRELKVSLPEVLEYLYNPCYDNFYTLYENLKSGKITFAEVDAIFKDFVDKYDELKNDLKFMCTMNPQDQKGWISERVGQIKEYHTLHQAVSSAKVILQVRRALGVTGDFSVLNPLLNFADSFEDFGNEKLDQISPQFIKAKQLLQDISEPRQRCLEELARQTELVAWLHKALEDINELKVFVDLASISAGENDIDVDRVACFHDAVQGYASLLYKMDERTNFSDFMNHLQELWRALDNDQHLPDKLKDSARNLEWLKTVKESHGSVELSSLSLATAINSRGVYVIEAPKDGQKISPDTVLRLLLPDGHGYPEALRTYSTEELKELLNKLMLMSGKKDHNSNTEVEKFSEVFSNMQRLVHVFIKLHCAGNMLFRTWTAKVYCCPDGGIFMNFGLELLSQLTEKGDVIQLLGALCRQMEDFLDNWKTVVAQKRAEHFYLNFYTAEQLVYLSSELRKPRPSEAALMMLSFIKGKCTVQDLVQATSACESKADRYCLREVMKKLPQQLLSEPSLMGKLQVIMMQSLVYMSAFLPHCLDLDALGRCLAHLATMGGTPVERPLPKGLQAGQPNLILCGHSEVLPAALAIYMQAPRQPLPTFDEVLLCTPATTIEEVELLLRRCLTSGSQGHKVYSLLFADQLSYEVGCQAEEFFQSLCTRAHREDYQLVILCDAAREHCYIPSTFSQYKVPLVPQAPLPNIQAYLQSHYQVPKRLLSAATVFRDGLCVGIVTSERAGVGKSLYVNTLHTKLKAKLRDETVPLKIIRLTEPHLDENQVLSALLPFLKEKYQKMPVIFHIDISTSVQTGIPIFLFKLLILQYLMDINGKIWRRSPGHLYLVEIPQGLSVQPKRSSKLNARAPLFKFLDLFPKVTCRPPKEVIDMELTPERSHTDPAMDPVEFCSEAFQRPYQYLKRFHQQQNLDTFQYEKGSVEGSPEECLQHFLIYCGLINPSWSELRNFAWFLNCQLKDCEASIFCKSAFTGDTLRGFKNFVVTFMILMARDFATPTLHTSDQSPGRQSVTIGEVVEEDLAPFSLRKRWESEPHPYVFFNGDHMTMTFIGFHLETNNNGYVDAINPSNGKVIKKDVMTKELFDGLRLQRVPFNIDFDNLPRYEKLERLCLALGIEWPIDPDETYELTTDNMLKILAIEMRFRCGIPVIIMGETGCGKTRLIKFLSDLKRGSVEAETMKLVKVHGGTTPSMIYSKVKEAERTAFSNKAQHKLDTILFFDEANTTEAVSCIKEILCDRTVDGEHLHEDSGLHIIAACNPYRKHSQEMILRLESAGLGYRVSAEETADRLGSIPLRQLVYRVHALPPSLIPLVWDFGQLNDSAEKLYIQQIVQRLVDSVSVNPSETCVIADVLSASQMFMRKRENECGFVSLRDVERCVKVFRWFHDHSDMLLKELDKFLHESSDSTHTFERDPVLWSLVMAIGVCYHASLEEKASYRTAIARCFPKPYNSSRAILDEVTHVQDLFLRGAPIRTNIARNLALKENVFMMVICIELKIPLFLVGKPGSSKSLAKIIVADAMQGQAAFSELFRCLKQVHLVSFQCSPHSTPQGIISTFKQCARFQQGKDLGQYVSVVVLDEVGLAEDSPKMPLKTLHPLLEDGCIEDDPAPYKKVGFVGISNWALDPAKMNRGIFVSRGSPNEKELIESAEGICSSDRLVQDKIRGYFAPFAKAYETVCQKQDKEFFGLRDYYSLIKMVFAKAKASKRGLSPQDITHAVLRNFSGKDNIQALSIFTASLPEARYKEEVSTVELIKQNIYPGPQASSRGLDGAESRYLLVLTRNYVALQILQQTFFEGQQPEIIFGSSFPQDQEYTQICRNINRVKICMETGKMVVLLNLQNLYESLYDALNQYYVYLGGQKYVDLGLGTHRVKCRVHTAFRLIVIEEKDVVYKQFPVPLINRLEKHYLDMNTVLQPWQKSIVQELQQWAHEFADVKADQFIARHKYSPADVFIGYHSDACASVVLQAVERQGCRDLTEELYRKVSEEARSILLDCATPDAVVRLSGSSLGSFTAKQLSQEYYYAQQHNSFVDFLQAHLRMTHHECRAVFTEITTFSRLLTGNDCDVLASELRGLASKPVVLSLQQYDTEYSFLKDVRSWLTNPGKRKVLVIQADFDDGTRSAQLVASAKYTAINEINKTQGTKDFVFVYFVTKLSRMGSGTSYVGFHGGLWRSVHIDDLRRSTIMASDVTKLQNVTISQLFKPEDKPEQEEMEIETSQSKELAEEQMEVEDSEEMKKASDPRSCDCSQFLDTTRLVQSCVQGAVGMLRDQNESCARNMRRVTILLDLLNEDNTRNASFLRESKMRLHVLLNKQEENQVRSLKEWVTREAANQDALQEAGTFRHTLWKRVQDVVTPILASMIAHIDRDGNLELLAQPDSPAWVQDLWMFIYSDIKFLNISLVLNNTRSNSEMSFILVQSHMNLLKDAYNAVPFSWRIRDYLEELWVQAQYITDTEGLSKKFVEIFQKTPLGVFLAQFPVAQQQKLLQSYLKDFLLLTMKVSSREELMFLQMALWSCLRELQEASGTPDETYKFPLSLPWVHLAFQHFRTRLQNFSRILTIHPQVLSSLSQAAEKHSLAGCEMTLDAFAAMACAEMLKGDLLKPSPKAWLQLVKNLSTPLELVCSEGYLCDSGSMTRSVIQEVRALWNRIFSIALFVEHVLLGTESHIPELSPLVTTYVSLLDKCLEEDSNLKTCRPFVAVMTTLCDCKDKASKKFSRFGIQPCFICHGDAQDPVCLPCDHVYCLRCIQTWLIPGQMMCPYCLTDLPDKFSPTVSQDHRKAIEKHAQFRHMCNSFFVDLVSTMCFKDNTPPEKSVIDTLLSLLFVQKELLRDASQKHREHTKSLSPFDDVVDQTPVIRSVLLKLLLKYSFHEVKDYIQNYLTQLEKKAFLTEDKTELYLLFISCLEDSVHQKTSAGCRNLEQVLREEGHFLRTYSPGLQGQEPVRIASVEYLQEVARVRLCLDLAADFLSELQEGSELAEDKRRFLKHVEEFCTRVNNDWHRVYLVRKLSSQRGMEFVQSFSKQGHPCQWVFPRKVIAQQKDHVSLMDRYLVHGNEYKAVRDATAKAVLECKTLDIGNALMACRSPKPQQTAYLLLALYTEVAALYRSPNGSLHPEAKQLEAVNKFIKESKILSDPNIRCFARSLVDNTLPLLKIRSANSILKGTVTEMAVHVATILLCGHNQILKPLRNLAFYPVNMANAFLPTMPEDLLVHARTWRGLENVTWYTCPRGHPCSVGECGRPMQESTCLDCGLPVGGLNHTPHEGFSAIRNNEDRTQTGHVLGSPQSSGVAEVSDRGQSPVVFILTRLLTHLAMLVGATHNPQALTVIIKPWVQDPQGFLQQHIQRDLEQLTKMLGRSADETIHVVHLILSSLLRVQSHGVLNFNAELSTKGCRNNWEKHFETLLLRELKHLDKNLPAINALISQDERISSNPVTKIIYGDPATFLPHLPQKSIIHCSKIWSCRRKITVEYLQHIVEQKNGKETVPVLWHFLQKEAELRLVKFLPEILALQRDLVKQFQNVSRVEYSSIRGFIHSHSSDGLRKLLHDRITIFLSTWNALRRSLETNGEIKLPKDYCCSDLDLDAEFEVILPRRQGLGLCGTALVSYLISLHNNMVYTVQKFSNEDNSYSVDISEVADLHVISYEVERDLNPLILSNCQYQVQQGGETSQEFDLEKIQRQISSRFLQGKPRLTLKGIPTLVYRRDWNYEHLFMDIKNKMAQSSLPNLAISTISGQLQSYSDACEALSIIEITLGFLSTAGGDPGMDLNVYIEEVLRMCDQTAQVLKAFSRCQLRHIIALWQFLSAHKSEQRLRLNKELFREIDVQYKEELSTQHQRLLGTFLNEAGLDAFLLELHEMIVLKLKGPRAANSFNPNWSLKDTLVSYMETKDSDILSEVESQFPEEILMSSCISVWKIAATRKWDRQSRGGGHHHHHHHHHH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Trichoplusia ni

Entity 2 polymer

描述 description	Ubiquitin-conjugating enzyme E2 L3
分子量 formula_weight	19197.9 kDa
EC 编号 ec_number	2.3.2.23
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

GWSHPQFEKPGSMAASRRLMKELEEIRKSGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKITFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFSKNAEEFTKKYGEKRPVD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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7. 引用文献 (2)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	3.800 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	3.80 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	31607

fit	/app/data/saxs_computation/i1/9i1j/9i1j.fit
pddf	/app/data/pr_computation/i1/9i1j/9i1j.pr.out
profile	/app/data/saxs_computation/i1/9i1j/9i1j.dat

Cryo-EM structure of mouse RNF213:UBE2L3 transthiolation intermediate, chemically stabilized, and ATPgS

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

冷冻电镜 EM 3D

5. 实体与聚合体信息 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)