8fmg

;Structure of CBASS Cap5 from Pseudomonas syringae as an activated tetramer with the cyclic dinucleotide 3'2'-c-diAMP ligand (3 tetramers in the AU) ;

Method: X-RAY DIFFRACTION D_max: 209.8 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	8fmg
沉积日期 deposition_date	2022-12-23
结构标题 title	;Structure of CBASS Cap5 from Pseudomonas syringae as an activated tetramer with the cyclic dinucleotide 3'2'-c-diAMP ligand (3 tetramers in the AU) ;
关键词 keywords	cyclic dinucleotide, bacterial immunity, CBASS, Cap5 effector DNA endonuclease, viral defense, IMMUNE SYSTEM; IMMUNE SYSTEM
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	69.95 Å
回转半径 Rg (电子) rg_electron	70.22 Å
零角强度 I(0) i0	3431810000.00
分子量 molecular_weight	482500.0 kDa
排除体积 excluded_volume	598460 Å³
包络体积 envelope_volume	901430 Å³
水化壳体积 shell_volume	110300 Å³
包络直径 envelope_diameter	229.6 Å
壳层 Rg shell_rg	65.76 Å
包络 Rg envelope_rg	68.43 Å
形状 Rg shape_rg	70.22 Å
总 Rg total_rg	70.15 Å
总原子数 total_atoms	66832
残基数 n_residues	4339
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	209.8 Å
Rg (实空间) rg_real	70.17 Å
Rg 误差 (实空间) rg_real_error	1.55 Å
I(0) (实空间) i0_real	3.4290e+09
I(0) 误差 (实空间) i0_real_error	7.2980e+07
Rg (倒空间) rg_reciprocal	68.65 Å
I(0) (倒空间) i0_reciprocal	3421000000.0000
解质量估计 total_estimate	0.8312
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	57.2 Å
偏度 Skewness skewness	0.419
峰度 Kurtosis kurtosis	-0.587
角度范围 angular_range	— – 0.1100 Å⁻¹
当前正则化参数 α current_alpha	0.0040
最高正则化参数 α highest_alpha	246700000.0000
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: 0.932; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.028

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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 (5)

Entity 1 polymer

描述 description	SAVED domain-containing protein
分子量 formula_weight	42769.2 kDa
来源方法 src_method	man
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,K,L,M,N
原子数 atom_count	69460

MAEKEDAKPASGRFNTNDETKRIVWTQTAGHCELCGTDLTFDYRAGKPMKWGEVAHILPASPKGPRGRADHDAEAHTNDTANLMLLCPGCHDKIDRDADGYPENDLSGLHQAYLERIRLAATTPDGGRAIPLIVQSQHFQTINDIPVRDLLTAMSAEGLTAFDQGIKIAFAAPGPRGRDTTYWQNVKDSVQYELEQQLKRRGGTYGDSPALAVVGLADIPALMMLGQSIGDRSKRLIFSFHREHLLRWPDQSAEPPSFLFTPPPNGDGPLALVLSISAQVPVRDVTDALPGARIAELSIPEPSYAMVQNRRVIHAFRDALQIRLSQLEALTPDPIHVFAAIPAALAIEFGALLTTQHQHTYLIFDRDKENQDRFTQTLQLGPVAQEAM

来源 Source

来源生物 organism	Pseudomonas syringae
NCBI 分类编号 ncbi_taxonomy_id	317
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	13

Entity 4 non-polymer

描述 description	;Cyclic (adenosine-(2'-5')-monophosphate-adenosine-(3'-5')-monophosphate ;
分子量 formula_weight	658.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 5 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	2474

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7. 引用文献 (1)

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晶胞边长 a length_a	145.192 Å
晶胞边长 b length_b	80.522 Å
晶胞边长 c length_c	406.841 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.62 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	48

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	monoclinic

分辨率 resolution	1.790 Å
最低分辨率 resolution_low	58.120 Å
R 因子 r_factor	0.1816
R_work r_work	0.1794
R_free r_free	0.2254

fit	/app/data/saxs_computation/fm/8fmg/8fmg.fit
pddf	/app/data/pr_computation/fm/8fmg/8fmg.pr.out
profile	/app/data/saxs_computation/fm/8fmg/8fmg.dat

;Structure of CBASS Cap5 from Pseudomonas syringae as an activated tetramer with the cyclic dinucleotide 3'2'-c-diAMP ligand (3 tetramers in the AU) ;

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