8h8b

Type VI secretion system effector RhsP in its pre-autoproteolysis and monomeric form

Method: ELECTRON MICROSCOPY D_max: 105.5 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8h8b
沉积日期 deposition_date	2022-10-22
结构标题 title	Type VI secretion system effector RhsP in its pre-autoproteolysis and monomeric form
关键词 keywords	T6SS, Rhs proteins, polymorphic toxins, 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	33.84 Å
回转半径 Rg (电子) rg_electron	32.83 Å
零角强度 I(0) i0	232052000.00
分子量 molecular_weight	117820.0 kDa
排除体积 excluded_volume	145760 Å³
包络体积 envelope_volume	212000 Å³
水化壳体积 shell_volume	53958 Å³
包络直径 envelope_diameter	113.0 Å
壳层 Rg shell_rg	40.34 Å
包络 Rg envelope_rg	31.21 Å
形状 Rg shape_rg	32.82 Å
总 Rg total_rg	33.50 Å
总原子数 total_atoms	8344
残基数 n_residues	1027
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	105.5 Å
Rg (实空间) rg_real	33.67 Å
Rg 误差 (实空间) rg_real_error	0.72 Å
I(0) (实空间) i0_real	2.3210e+08
I(0) 误差 (实空间) i0_real_error	3.4770e+06
Rg (倒空间) rg_reciprocal	33.77 Å
I(0) (倒空间) i0_reciprocal	232100000.0000
解质量估计 total_estimate	0.8949
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	47.1 Å
偏度 Skewness skewness	0.145
峰度 Kurtosis kurtosis	-0.413
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	79450000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.988

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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 (1)

Entity 1 polymer

描述 description	Putative Rhs-family protein
分子量 formula_weight	160008.5 kDa
突变 mutation	E161A/D1127A/H1354A
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	8344

MGSSHHHHHHSQDPENLYFQSMIPQFVIPLTNCLGQSYHFSSQPIPKGEHKKFDSEQSAKAFLDDFVPLRSSRVEELYHLLGQFPPNVPDEELTPELYAPVFAKALVNGSLYVASFPKTKKNATISSEPTPVPKQVKAKSKQNKAHTSSKTQAKNSASAKPLQTGSECHEKAGDPVSLVTGAEILTLNDVELPNGFVWSRTYRSSKASRNQGLGYGWRHAFQFELKEVTDEKHNVTSWEFISDSADEIEFEPVEHGSTSYQVYVGASCHFLNPNIRIVTLSSGDQYRFELVEDIWLLKQVRNGIFSTFQLRYSRNHRLIEVAHNKRPVLECQYDKQGRLVELLNAKTEQVLTTYIYDEQDDLVGATNDLGLTERYEYQDQHLIAKRVRPTGFTHYFEWSGEGSSAKCIRNFGDSGIYDYRFHYEGAKSSYSDSLDNEWTFIHDEQGHLLEKSSPTGRTWQWHYDHLGRKEKAVFPDNSTTQYQYNQQGQLISKLHSSGAQIQYGYDSLGKLVKTVSPDGDLEKAYYNSLGQRVWDIDALGCVTEYEYDKHGQVVKRESEDGKKSRWWWDKQQRLVAHEVDGTLLRYSYGATDLVNGIAYPDGCVAQISYDDYGRRTSIRYFNDEDKVGYSEEYAYDEFSRVAQIQTPEGVTSYQWGALAQQEAVIFPDGSHISYEYDQQRNLTKLVRSDGLAFEFWYDSEGLLSGTVGFDGLHSQFKYDSMGRIIRKDVADRTVLYSYDDAGFLQHIKAGNGKNIVENHFNYTLGGRLTLASNRHQTLQYQYSSFGHLTKRIQGQFEIGEEFNRVGQRVSQTLPDKTSFNFSYDTNGRLSEIRFSDDSLPKIEFQYDVMGRLSVTETESFRESKLYDGVGRLVEQQWSGREKKYIYNAQNRISSILDNTAGATHYQYDTLGYVTKVSEAGSTSTFESDSFGNPALADSKVMSDRIEAYAGVRYKYDQQGNQVKREGDGTVQKRVFDALSQLVEVHGDSSISHYEYDALGRRTKKITQNGITEFLWEGERLLGERTADGFRWYLYQPETYIPLAVLENGSIYLYECDQVGKPERLKDSAGNIVWSASYDVHGFASIDVEEVRNPLRFQGQYFDQETNLHYNLARYYDPKLGRFIQQDPISIAGGINHYQYAVNPIQWIAPTGFLCEEGLKRLQQMLAEYQAQSDVPQEVCDQILEAAKESSVGEDGVRSQVKIRKPNGKNNIRYEYDLDHIDCKKNEITFYRHINYSDGSKRKIQYTVGIEGFVDIYDFVNVQKCDAQVYDTKTSKTVGGRKIINSEFAGKTVTTKGGDVRFDSDGFPDFTPYSKKTVRVIGLTGDMANDVPLAMARAKITKYDKSKYVWHHHQDGKTMMLIPKSVHSVRNGGVAATGGRSVIQHNLLNPNNKLNYSSPEELV

来源 Source

来源生物 organism	Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
NCBI 分类编号 ncbi_taxonomy_id	223926
宿主生物 host_organism	Escherichia coli BL21(DE3)

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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	3.16 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	738487

fit	/app/data/saxs_computation/h8/8h8b/8h8b.fit
pddf	/app/data/pr_computation/h8/8h8b/8h8b.pr.out
profile	/app/data/saxs_computation/h8/8h8b/8h8b.dat

Type VI secretion system effector RhsP in its pre-autoproteolysis and monomeric form

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 (1)

Entity 1 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)