SAXSdb — 8w22

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8w22
沉积日期 deposition_date	2024-02-19
结构标题 title	Umb1 umbrella toxin particle (local refinement of UmbB1 bound ALF of UmbC1 and UmbA1)
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	37.42 Å
回转半径 Rg (电子) rg_electron	38.12 Å
零角强度 I(0) i0	52994600.00
分子量 molecular_weight	52833.0 kDa
排除体积 excluded_volume	63922 Å³
包络体积 envelope_volume	106360 Å³
水化壳体积 shell_volume	27588 Å³
包络直径 envelope_diameter	140.0 Å
壳层 Rg shell_rg	36.09 Å
包络 Rg envelope_rg	39.27 Å
形状 Rg shape_rg	38.14 Å
总 Rg total_rg	37.89 Å
总原子数 total_atoms	3750
残基数 n_residues	629
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	142.3 Å
Rg (实空间) rg_real	38.31 Å
Rg 误差 (实空间) rg_real_error	2.13 Å
I(0) (实空间) i0_real	5.2990e+07
I(0) 误差 (实空间) i0_real_error	1.0260e+06
Rg (倒空间) rg_reciprocal	37.76 Å
I(0) (倒空间) i0_reciprocal	52970000.0000
解质量估计 total_estimate	0.6106
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	23.7 Å
偏度 Skewness skewness	0.701
峰度 Kurtosis kurtosis	-0.191
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9217000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.257; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.162; 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 (3)

Entity 1 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
原子数 atom_count	3750

MRRRIPSRTPGSGAKQKSWFPRRSLQVLLSAGMLSGLLGTPAALAAEPAPLPANVRADIVGYWETGGAGLKAAAEQALLGGDEAIRKFLADAPSIQHDDNRIDAARMAMTGGSGLRQAAKDAIRLSPAELEKFLLYGYEEPLDDDHKVEIARLINLGGPGVREAGKAALQGTAEERELFLNSGQYTAQQDDNRVDVARLATTGGPNVQAAAKVALRGTPEDMVEFLEVGQFTARNRDQEHATIAELIKQAELAGKQADDARKTAEESSKKAVDASQLAKEAAQKAAEETEAAKDDSQKAAVKAKQAADAARAAADAAQEAIGSANAANRAARRAALAAAQTASAATAAAEAANKAYKAAIAAAGDEGKADEAKEAAKQARAAADAATKSGLAAENAGLASAAAATASTAAKSASSNARAAAGAAEEANQHADAAGVHSNEAALAAAEARRHADAADRAADRSSALAQRAATAAYGARDAANSAAEHANKAADYADESAAHAGDSAAYAATAKRNAQAAQEAAKTATAAVTKANEIFKLARETETANLETRTDAAIERARSMKSASETSITASATTQVEALALNDTATELAKEASRPDIDVQATAAKGRQLAMQAMKLLGPWHQEAAARALSGTDQDVLDYLRTRWKEANHNDIRQQIVDLSTQSPYASVRTAAAEALNGTPEQIEAFHTTGQYTAGSDDMKVDVARLANTGGPGVSQAAKTALADGTGKTLATFLQIGQYGERLSDEKVVTARLAETGSPEVQAAAKIALAGPPELLHEFVTTGQYMAKRKDDLADVHVNQVERLLAEGSLIAAEANEDAWRATEAAATAEGAAADAATAAEKAEASAAQAKQHAADADASADAATRSAADAAASAATARDAADRAAQDATAAENSAAEAAFSAAYARDSASKADDAADRARASALAAGKSADEAEAEAKEAWKTTRALAEKEAEEARRKAAEERKRQQEQAGEPKRVCIPHPTRETMIPIMPCAASPDDSMIMPGPVDPTIRAVVWELAGLNDIKACIDKPLSGNCVMAVVGVTPWGKFKLVSKLGNGLDAVKDARGARRTVACLTGAAHSFPAGTRVLMADGTRRSIEQIEAGDLVTATDPTTGETGARTVTRTIHTPDDRNFTDVALADGSTLTSTTHHPYWSQNDQTWKNAGDLEAGDTLRTPQNTAVVIAATHDWPGLQDAYDLTVDGFHSYYVSTGTTDVLVHNNDNPCPDWVSKAWKKLPKRKSGDPTSGYVFEADGTLVWDSVLTSGRSPLSEDISAFLKGSPDFPNFPGYADVAHHAEAKIAWEMRTKMGKGKKLHIVINTNYVCPKVSSPNSMGCKQAVPAILYEDQTLYVHYPGASDALELKGTAKR

Entity 2 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	1

聚合体 Polymer

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

MANTSRTRQALMAIAVSVLAAGVTTLGVAHADNGDAVAAAAEMPQAVEDFSYPGAAKIQAETGAILKRGNGHMLMTSCDGSEDIQVMSRTGQKDFCFNVMAKPAYLTLEVPQAYGIWTSADPVKTTIKDTDGTATVINAPANDFTGYGEAGSTGEPTTLIELRVAG

Entity 3 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	1

聚合体 Polymer

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

MFRMPRPIRATALSAAVLAGALASTPAQATVGDPTTDAKLDFTARLTIGTDYRSCSGALVDTQWVLTAASCFADDPNQPDTVAAGKPAQLTRATVGRADSNIANGYVREVVELVPHPERDMVLARLDKAIPDIAPVRLASDAPTAGTPLTAVGFGRTKDEWVPIQRHQGAFTVTSVTAGAVNVTGQGGDAICAGDTGGPLLQDKNGTLHLVGVNNRSMQGGCYGSETTSTDAIAAMSDADFVTQTVNRDLGTGNLSDLVASADFNSDGRTDVAAVLEDGSLHAFYAKPDGTLEYGRELWNDNTWSPMVQIIGGDFNSDGNGDIAAVRSDGTLNLYTGTATGILNKSKPMWHDTSWKTIKQVTRFKFNGRDGLVAQWGDGNLYGYYTGTDGTLTGTKVKMWPDATWGKTRLTGTADINADGRDDLTAVRDDGSLNWYAGNTKGGLDAARKLWPDNTWTPMKRIIGGDFNGDNKGDIAAVGGQSTLLLYTGTGTGTLNKGIAMRPASGSHHHHHHHH

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

fit	/app/data/saxs_computation/w2/8w22/8w22.fit
pddf	/app/data/pr_computation/w2/8w22/8w22.pr.out
profile	/app/data/saxs_computation/w2/8w22/8w22.dat

Umb1 umbrella toxin particle (local refinement of UmbB1 bound ALF of UmbC1 and UmbA1)

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

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)