SAXSdb — 8y6q

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8y6q
沉积日期 deposition_date	2024-02-03
最后修订 last_revision	2024-08-07
结构标题 title	Structure of the Dark/Dronc complex
关键词 keywords	Dark, Dronc, apoptosis, cryo-EM; APOPTOSIS
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	96.08 Å
回转半径 Rg (电子) rg_electron	96.12 Å
零角强度 I(0) i0	15058700000.00
分子量 molecular_weight	1076400.0 kDa
排除体积 excluded_volume	1358600 Å³
包络体积 envelope_volume	2495800 Å³
水化壳体积 shell_volume	209860 Å³
包络直径 envelope_diameter	308.9 Å
壳层 Rg shell_rg	98.62 Å
包络 Rg envelope_rg	92.85 Å
形状 Rg shape_rg	96.12 Å
总 Rg total_rg	96.13 Å
总原子数 total_atoms	75726
残基数 n_residues	9362
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	247.1 Å
Rg (实空间) rg_real	92.60 Å
Rg 误差 (实空间) rg_real_error	0.73 Å
I(0) (实空间) i0_real	1.4450e+10
I(0) 误差 (实空间) i0_real_error	2.6480e+08
Rg (倒空间) rg_reciprocal	95.45 Å
I(0) (倒空间) i0_reciprocal	15020000000.0000
解质量估计 total_estimate	0.9142
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	92.7 Å
偏度 Skewness skewness	0.132
峰度 Kurtosis kurtosis	-0.775
角度范围 angular_range	— – 0.0800 Å⁻¹
当前正则化参数 α current_alpha	0.6454
最高正则化参数 α highest_alpha	1937000000.0000
实空间数据点数 n_real_points	17
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.998; Stabil: 0.964; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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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 (2)

Entity 1 polymer

描述 description	Apaf-1 related killer DARK
分子量 formula_weight	142710.3 kDa
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H,J,L,M,O,Q,I,K
原子数 atom_count	75726

YQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQVQRFDDRVWFTNHGRFHQHRQIINLGDNEGRHAVYLHNDFCLIALASGQILLTDVSLEGEDTYLLRDESDSSDILRMAVFNQQKHLITLHCNGSVKLWSLWPDCPGRRHSGGSKQQLVNSVVKRFIGSYANLKIVAFYLNEDAGLPEANIQLHVAFINGDVSILNWDEQDQEFKLSHVPVLKTMQSGIRCFVQVLKRYYVVCTSNCTLTVWDLTNGSSNTLELHVFNVENDTPLALDVFDERSKTATVLLIFKYSVWRLNFLPGLSVSLQSEAVQLPEGSFITCGKRSTDGRYLLLGTSEGLIVYDLKISDPVLRSNVSEHIECVDIYELFDPVYKYIVLCGAKGKQVVHVHTLRSVSGSNSHQNREIAWVHSADEISVMTKACLEPNVYLRSLMDMTRERTQLLAVDSKERIHLIKPAISRISEWSTITPTHAASNCKINAISAFNDEQIFVGYVDGVIIDVIHDTALPQQFIEEPIDYLKQVSPNILVASAHSAQKTVIFQLEKIDPLQPNDQWPLMMDVSTKYASLQEGQYIILFSDHGVCHLDIANPSAFVKPKDSEEYIVGFDLKNSLLFLAYENNIIDVFRLIFSCNQLRYEQICEEEIAQKAKISYLVATDDGTMLAMGFENGTLELFAVENRKVQLIYSIEEVHEHCIRQLLFSPCKL

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	fruit fly
NCBI 分类编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 polymer

描述 description	Caspase Dronc
分子量 formula_weight	12040.0 kDa
EC 编号 ec_number	3.4.22.-
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	N,A,B,C,D,E,F,G

MPKRHREHIRKNLNILVEWTNYERLAMECVQQGILTVQMLRNTQDLNGKPFNMDEKDVRVEQHRRLLLKITQRGPTAYNLLINALRNINCLDAAVLLESVDE

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	fruit fly
NCBI 分类编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli

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7. 引用文献 (1)

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分辨率 resolution	7.00 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	2710

fit	/app/data/saxs_computation/y6/8y6q/8y6q.fit
pddf	/app/data/pr_computation/y6/8y6q/8y6q.pr.out
profile	/app/data/saxs_computation/y6/8y6q/8y6q.dat

Structure of the Dark/Dronc complex

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)