SAXSdb — 8w20

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8w20
沉积日期 deposition_date	2024-02-19
结构标题 title	Umb1 umbrella toxin particle
关键词 keywords	;Streptomyces, Umbrella toxin particles, Alanine leucine phenylalanine-rich (ALF) repeat proteins, Seattle structural genomics center for infectious disease, SSGCID, TOXIN ;; TOXIN
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	72.02 Å
回转半径 Rg (电子) rg_electron	71.52 Å
零角强度 I(0) i0	866195000.00
分子量 molecular_weight	216830.0 kDa
排除体积 excluded_volume	258010 Å³
包络体积 envelope_volume	531280 Å³
水化壳体积 shell_volume	69974 Å³
包络直径 envelope_diameter	242.4 Å
壳层 Rg shell_rg	57.67 Å
包络 Rg envelope_rg	71.09 Å
形状 Rg shape_rg	71.61 Å
总 Rg total_rg	70.90 Å
总原子数 total_atoms	15412
残基数 n_residues	2814
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	216.1 Å
Rg (实空间) rg_real	72.05 Å
Rg 误差 (实空间) rg_real_error	1.44 Å
I(0) (实空间) i0_real	8.6540e+08
I(0) 误差 (实空间) i0_real_error	1.5160e+07
Rg (倒空间) rg_reciprocal	71.23 Å
I(0) (倒空间) i0_reciprocal	864500000.0000
解质量估计 total_estimate	0.6116
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	78.6 Å
偏度 Skewness skewness	0.312
峰度 Kurtosis kurtosis	-0.461
角度范围 angular_range	— – 0.1100 Å⁻¹
当前正则化参数 α current_alpha	0.0043
最高正则化参数 α highest_alpha	34650000.0000
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: 0.968; Stabil: 0.999; Sysdev: 0.006; Positv: 1.000; Valcen: 0.997; Smooth: 0.030

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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	Secreted protein
分子量 formula_weight	17186.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D,F,H,J
原子数 atom_count	15412

MANTSRTRQALMAIAVSVLAAGVTTLGVAHADNGDAVAAAAEMPQAVEDFSYPGAAKIQAETGAILKRGNGHMLMTSCDGSEDIQVMSRTGQKDFCFNVMAKPAYLTLEVPQAYGIWTSADPVKTTIKDTDGTATVINAPANDFTGYGEAGSTGEPTTLIELRVAG

Entity 2 polymer

描述 description	Secreted esterase
分子量 formula_weight	54437.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,E,G,I,K

MFRMPRPIRATALSAAVLAGALASTPAQATVGDPTTDAKLDFTARLTIGTDYRSCSGALVDTQWVLTAASCFADDPNQPDTVAAGKPAQLTRATVGRADSNIANGYVREVVELVPHPERDMVLARLDKAIPDIAPVRLASDAPTAGTPLTAVGFGRTKDEWVPIQRHQGAFTVTSVTAGAVNVTGQGGDAICAGDTGGPLLQDKNGTLHLVGVNNRSMQGGCYGSETTSTDAIAAMSDADFVTQTVNRDLGTGNLSDLVASADFNSDGRTDVAAVLEDGSLHAFYAKPDGTLEYGRELWNDNTWSPMVQIIGGDFNSDGNGDIAAVRSDGTLNLYTGTATGILNKSKPMWHDTSWKTIKQVTRFKFNGRDGLVAQWGDGNLYGYYTGTDGTLTGTKVKMWPDATWGKTRLTGTADINADGRDDLTAVRDDGSLNWYAGNTKGGLDAARKLWPDNTWTPMKRIIGGDFNGDNKGDIAAVGGQSTLLLYTGTGTGTLNKGIAMRPASGSHHHHHHHH

Entity 3 polymer

描述 description	Intein C-terminal splicing domain-containing protein
分子量 formula_weight	142716.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

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

MRRRIPSRTPGSGAKQKSWFPRRSLQVLLSAGMLSGLLGTPAALAAEPAPLPANVRADIVGYWETGGAGLKAAAEQALLGGDEAIRKFLADAPSIQHDDNRIDAARMAMTGGSGLRQAAKDAIRLSPAELEKFLLYGYEEPLDDDHKVEIARLINLGGPGVREAGKAALQGTAEERELFLNSGQYTAQQDDNRVDVARLATTGGPNVQAAAKVALRGTPEDMVEFLEVGQFTARNRDQEHATIAELIKQAELAGKQADDARKTAEESSKKAVDASQLAKEAAQKAAEETEAAKDDSQKAAVKAKQAADAARAAADAAQEAIGSANAANRAARRAALAAAQTASAATAAAEAANKAYKAAIAAAGDEGKADEAKEAAKQARAAADAATKSGLAAENAGLASAAAATASTAAKSASSNARAAAGAAEEANQHADAAGVHSNEAALAAAEARRHADAADRAADRSSALAQRAATAAYGARDAANSAAEHANKAADYADESAAHAGDSAAYAATAKRNAQAAQEAAKTATAAVTKANEIFKLARETETANLETRTDAAIERARSMKSASETSITASATTQVEALALNDTATELAKEASRPDIDVQATAAKGRQLAMQAMKLLGPWHQEAAARALSGTDQDVLDYLRTRWKEANHNDIRQQIVDLSTQSPYASVRTAAAEALNGTPEQIEAFHTTGQYTAGSDDMKVDVARLANTGGPGVSQAAKTALADGTGKTLATFLQIGQYGERLSDEKVVTARLAETGSPEVQAAAKIALAGPPELLHEFVTTGQYMAKRKDDLADVHVNQVERLLAEGSLIAAEANEDAWRATEAAATAEGAAADAATAAEKAEASAAQAKQHAADADASADAATRSAADAAASAATARDAADRAAQDATAAENSAAEAAFSAAYARDSASKADDAADRARASALAAGKSADEAEAEAKEAWKTTRALAEKEAEEARRKAAEERKRQQEQAGEPKRVCIPHPTRETMIPIMPCAASPDDSMIMPGPVDPTIRAVVWELAGLNDIKACIDKPLSGNCVMAVVGVTPWGKFKLVSKLGNGLDAVKDARGARRTVACLTGAAHSFPAGTRVLMADGTRRSIEQIEAGDLVTATDPTTGETGARTVTRTIHTPDDRNFTDVALADGSTLTSTTHHPYWSQNDQTWKNAGDLEAGDTLRTPQNTAVVIAATHDWPGLQDAYDLTVDGFHSYYVSTGTTDVLVHNNDNPCPDWVSKAWKKLPKRKSGDPTSGYVFEADGTLVWDSVLTSGRSPLSEDISAFLKGSPDFPNFPGYADVAHHAEAKIAWEMRTKMGKGKKLHIVINTNYVCPKVSSPNSMGCKQAVPAILYEDQTLYVHYPGASDALELKGTAKR

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7. 引用文献 (1)

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分辨率 resolution	4.30 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	386275

fit	/app/data/saxs_computation/w2/8w20/8w20.fit
pddf	/app/data/pr_computation/w2/8w20/8w20.pr.out
profile	/app/data/saxs_computation/w2/8w20/8w20.dat

Umb1 umbrella toxin particle

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 (3)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)