8qjb

T6SS-linked Rhs repeat protein - Salmonella bongori Rhs-core domain extended N-terminus

Method: X-RAY DIFFRACTION D_max: 159.6 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	8qjb
沉积日期 deposition_date	2023-09-13
结构标题 title	T6SS-linked Rhs repeat protein - Salmonella bongori Rhs-core domain extended N-terminus
关键词 keywords	Rhs, T6SS, PAAR-Rhs, toxin cannister, Rhs-repeat, CELL INVASION; CELL INVASION
实验方法 method	X-RAY DIFFRACTION

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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	49.22 Å
回转半径 Rg (电子) rg_electron	49.06 Å
零角强度 I(0) i0	930578000.00
分子量 molecular_weight	238780.0 kDa
排除体积 excluded_volume	292700 Å³
包络体积 envelope_volume	453060 Å³
水化壳体积 shell_volume	78040 Å³
包络直径 envelope_diameter	169.5 Å
壳层 Rg shell_rg	52.24 Å
包络 Rg envelope_rg	47.40 Å
形状 Rg shape_rg	49.04 Å
总 Rg total_rg	49.23 Å
总原子数 total_atoms	16862
残基数 n_residues	2074
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	159.6 Å
Rg (实空间) rg_real	49.34 Å
Rg 误差 (实空间) rg_real_error	1.59 Å
I(0) (实空间) i0_real	9.3060e+08
I(0) 误差 (实空间) i0_real_error	1.9230e+07
Rg (倒空间) rg_reciprocal	49.22 Å
I(0) (倒空间) i0_reciprocal	930400000.0000
解质量估计 total_estimate	0.8537
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	54.9 Å
偏度 Skewness skewness	0.374
峰度 Kurtosis kurtosis	-0.411
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	58770000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.365

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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	T6SS-associated Rhs core domain
分子量 formula_weight	123894.8 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	16862

GSGSDGVNSMLCTKSGEPVDIGTGDFLQHFSVLSLPGSLPLTLSRFYRSQAKGTGIFGPKWTDEWSCMLTVHGNDMHFTNHEGVDLYYRIPQNGIFRDTANSRQAYYRLSGDIRDELTIFDRRSQHSQIFSLTDNGIYLLSAIHDRYGNRADFIRTEGLLTGIHHSDGYTLALGWQQRQLVSIDLATPQRQRLVTCHYDKNGYLAECDTIQFSHLWHEYTSEGWMTRWRDTDKTCVDIVYDTLGRTVSTLSTEGYFDDQFLYNDDEKCTTYLDAEGGETRYWYNGDGLVTRSIDPLGREETSVWENTRLRSRTDALGRTTAYDYNNEGEISRVSLPGGYSLYYDYNEHGQLTRLSAPGNQVWLWEYDGKGSMVCLTDPQGRQQQFSYSEHGDLLRQIMPNGATWRWSHDALHQVRATTAPDGGVTQTEQDILGRLLSVKDPLGYTTQFRYSKNHAGPQGSVEEIRRPDGVRELMRQNSEKLPESFTDGEGNTTRYEYGAFDLLTAVIRPDGERLACRYDKLTRLTEITNAEGEHYRLRYDKAGQLVAETDFTGRTLTYSYDAAGRCIRTTFPDGTHLNRQYSTTDQVTREEVAQGDSDRVLSCTTFIYDALSRLTEARNNDATVTYEYDDASRVTAETINGRRTEYNYDPDQDTVSQRTTAGITECFTRGLTGELTQWQIDGHTPLTLEHDLRGQEISRQSEAGFSLRQNYTPTGMLTGQQAGDLTEQNPHYWRNNTLQRQWLYDKAYNLTMISDSLRGTMVNSVTANDQISHATWTGSSDIPMREERFAYDRNLNITRRQTQVNGVPDSEAYQHQQHGRVTSREYKAWRHTTTRINPDSGMPEEGQFVRVIRDEQTTWKYDVNGRLVEKLIDKGGYRPLRWRYRWDARSQLTGLETPEGERREYKYDPFGRRISKRCTNRDRPGTDFHWNGDQLTEEIPVGTDGTPEYENAIRWIYEPGSFTPLARYEKGQLHYTITDTVGRIQELLTEDGTIVWRGKQHLWGREEGRNKDDAPSCRLRFPGQYEDEESGLYYNRFRYYDCEAGQYLCADPIGLRGGINLYAYAPNPLSWIDPLGL

来源 Source

来源生物 organism	Salmonella bongori N268-08
NCBI 分类编号 ncbi_taxonomy_id	1197719
宿主生物 host_organism	Escherichia coli B

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7. 引用文献 (1)

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晶胞边长 a length_a	102.734 Å
晶胞边长 b length_b	118.733 Å
晶胞边长 c length_c	130.651 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	105.81 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	monoclinic

分辨率 resolution	3.090 Å
最低分辨率 resolution_low	47.500 Å
R 因子 r_factor	0.1874
R_work r_work	0.1853
R_free r_free	0.2268

fit	/app/data/saxs_computation/qj/8qjb/8qjb.fit
pddf	/app/data/pr_computation/qj/8qjb/8qjb.pr.out
profile	/app/data/saxs_computation/qj/8qjb/8qjb.dat

T6SS-linked Rhs repeat protein - Salmonella bongori Rhs-core domain extended N-terminus

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

精修参数 Refinement

衍射实验 Diffraction

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)