SAXSdb — 8pd0

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8pd0
沉积日期 deposition_date	2023-06-11
最后修订 last_revision	2024-01-17
结构标题 title	cryo-EM structure of Doa10 in MSP1E3D1
关键词 keywords	ERAD, Doa10, March6, TEB4, retrotranslocation, ubiquitination, Ubc6, sybody, SQLE, squalenemonooxygenase, 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	38.54 Å
回转半径 Rg (电子) rg_electron	36.50 Å
零角强度 I(0) i0	111446000.00
分子量 molecular_weight	88574.0 kDa
排除体积 excluded_volume	112820 Å³
包络体积 envelope_volume	190540 Å³
水化壳体积 shell_volume	44949 Å³
包络直径 envelope_diameter	138.1 Å
壳层 Rg shell_rg	41.22 Å
包络 Rg envelope_rg	36.11 Å
形状 Rg shape_rg	36.61 Å
总 Rg total_rg	36.56 Å
总原子数 total_atoms	6274
残基数 n_residues	880
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	129.2 Å
Rg (实空间) rg_real	38.49 Å
Rg 误差 (实空间) rg_real_error	1.19 Å
I(0) (实空间) i0_real	1.1140e+08
I(0) 误差 (实空间) i0_real_error	1.9930e+06
Rg (倒空间) rg_reciprocal	38.52 Å
I(0) (倒空间) i0_reciprocal	111400000.0000
解质量估计 total_estimate	0.8695
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	50.4 Å
偏度 Skewness skewness	0.300
峰度 Kurtosis kurtosis	-0.117
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9397000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.876

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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 (3)

Entity 1 polymer

描述 description	ERAD-associated E3 ubiquitin-protein ligase DOA10
分子量 formula_weight	151608.1 kDa
EC 编号 ec_number	2.3.2.27
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	6274

MDVDSDVNVSRLRDELHKVANEETDTATFNDDAPSGATCRICRGEATEDNPLFHPCKCRGSIKYMHESCLLEWVASKNIDISKPGADVKCDICHYPIQFKTIYAENMPEKIPFSLLLSKSILTFFEKARLALTIGLAAVLYIIGVPLVWNMFGKLYTMMLDGSSPYPGDFLKSLIYGYDQSATPELTTRAIFYQLLQNHSFTSLQFIMIVILHIALYFQYDMIVREDVFSKMVFHKIGPRLSPKDLKSRLKERFPMMDDRMVEYLAREMRAHDENRQEQGHDRLNMPAAAADNNNNVINPRNDNVPPQDPNDHRNFENLRHVDELDHDEATEEHENNDSDNSLPSGDDSSRILPGSSSDNEEDEEAEGQQQQQQPEEEADYRDHIEPNPIDMWANRRAQNEFDDLIAAQQNAINRPNAPVFIPPPAQNRAGNVDQDEQDFGAAVGVPPAQANPDDQGQGPLVINLKLKLLNVIAYFIIAVVFTAIYLAISYLFPTFIGFGLLKIYFGIFKVILRGLCHLYYLSGAHIAYNGLTKLVPKVDVAMSWISDHLIHDIIYLYNGYTENTMKHSIFIRALPALTTYLTSVSIVCASSNLVSRGYGRENGMSNPTRRLIFQILFALKCTFKVFTLFFIELAGFPILAGVMLDFSLFCPILASNSRMLWVPSICAIWPPFSLFVYWTIGTLYMYWFAKYIGMIRKNIIRPGVLFFIRSPEDPNIKILHDSLIHPMSIQLSRLCLSMFIYAIFIVLGFGFHTRIFFPFMLKSNLLSVPEAYKPTSIISWKFNTILLTLYFTKRILESSSYVKPLLERYWKTIFKLCSRKLRLSSFILGKDTPTERGHIVYRNLFYKYIAAKNAEWSNQELFTKPKTLEQAEELFGQVRDVHAYFVPDGVLMRVPSSDIVSRNYVQTMFVPVTKDDKLLKPLDLERIKERNKRAAGEFGYLDEQNTEYDQYYIVYVPPDFRLRYMTLLGLVWLFASILMLGVTFISQALINFVCSFGFLPVVKLLLGERNKVYVAWKELSDISYSYLNIYYVCVGSVCLSKIAKDILHFTEGQNTLDEHAVDENEVEEVEHDIPERDINNAPVNNINNVEEGQGIFMAIFNSIFDSMLVKYNLMVFIAIMIAVIRTMVSWVVLTDGILACYNYLTIRVFGNSSYTIGNSKWFKYDESLLFVVWIISSMVNFGTGYKSLKLFFRNRNTSKLNFLKTMALELFKQGFLHMVIYVLPIIILSLVFLRDVSTKQIIDISHGSRSFTLSLNESFPTWTRMQDIYFGLLIALESFTFFFQATVLFIQWFKSTVQNVKDEVYTKGRALENLPDES

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Trichoplusia ni

Entity 2 non-polymer

描述 description	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
分子量 formula_weight	787.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE
分子量 formula_weight	647.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (1)

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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	3.58 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	123143

fit	/app/data/saxs_computation/pd/8pd0/8pd0.fit
pddf	/app/data/pr_computation/pd/8pd0/8pd0.pr.out
profile	/app/data/saxs_computation/pd/8pd0/8pd0.dat

cryo-EM structure of Doa10 in MSP1E3D1

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

冷冻电镜 EM 3D