8y3y

The Cryo-EM structure of anti-phage defense associated DSR2 tetramer bound with two DSAD1 inhibitors (opposite side)

Method: ELECTRON MICROSCOPY D_max: 232.2 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	8y3y
沉积日期 deposition_date	2024-01-29
最后修订 last_revision	2024-09-11
结构标题 title	The Cryo-EM structure of anti-phage defense associated DSR2 tetramer bound with two DSAD1 inhibitors (opposite side)
关键词 keywords	NADase, anti-phage defense, complex, immune evasion, IMMUNOSUPPRESSANT; IMMUNOSUPPRESSANT
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	75.60 Å
回转半径 Rg (电子) rg_electron	77.01 Å
零角强度 I(0) i0	2914370000.00
分子量 molecular_weight	475140.0 kDa
排除体积 excluded_volume	601430 Å³
包络体积 envelope_volume	952840 Å³
水化壳体积 shell_volume	111820 Å³
包络直径 envelope_diameter	269.6 Å
壳层 Rg shell_rg	62.50 Å
包络 Rg envelope_rg	77.07 Å
形状 Rg shape_rg	76.98 Å
总 Rg total_rg	76.86 Å
总原子数 total_atoms	33586
残基数 n_residues	4034
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	232.2 Å
Rg (实空间) rg_real	75.09 Å
Rg 误差 (实空间) rg_real_error	1.53 Å
I(0) (实空间) i0_real	2.8930e+09
I(0) 误差 (实空间) i0_real_error	6.2300e+07
Rg (倒空间) rg_reciprocal	72.33 Å
I(0) (倒空间) i0_reciprocal	2890000000.0000
解质量估计 total_estimate	0.7905
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	55.3 Å
偏度 Skewness skewness	0.590
峰度 Kurtosis kurtosis	-0.470
角度范围 angular_range	— – 0.1050 Å⁻¹
当前正则化参数 α current_alpha	0.0551
最高正则化参数 α highest_alpha	263200000.0000
实空间数据点数 n_real_points	22
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.719; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.135

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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 (2)

Entity 1 polymer

描述 description	SIR2-like domain-containing protein
分子量 formula_weight	118635.8 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,D,E
原子数 atom_count	33586

MVKVDLESKRYGEKLKEVFLMLDNNVVECIKEITESSRNGKLVFFVGAGVSTLSDYPQWWRLVDKYHEELYGSPKKGNYSSDEYLRIPQIFYNVKGEMAFDGILKDFFQVDKPTNPIHDKILAMNPAHVITTNYDNLIDTACWKRGKYFSVISAEEDVANATSSRYLLKVHGDFRKGFKGENVVLKEDDYLNYDQNYPLISNLMKTIIATHTIVFIGYGLGDYNINMLLNWVRKLQKDSFHKPFFIRTDPSPIENETLIYYENKGLRIIDAASLIDSNEYDYLERYSAVMDLLIESQENKFITKDDEVIDYIYGKISPLFALQYIRKIDLKHVFEYDYHFEVNGTVVRHKNKGFGYMERFFELKESCDERSKLSKKQYERFNALFNFFEKNGVICMAKDAGTLNTSIEINSLAYHGKYDVMKKFIEEQSVSIEDDYKKAFFLACLGRWEESYDLYSNIILNSIDESNGCVYYLSQINRYRIYQSITQAVTQFNGLGLLTFGRHYKPFTDEFLARIEREMTNFNIDDLFNGMPFEFQKKYKILEFLSDNQFLYDDTVKLFELTNKVRSEMSEGSYSFGMSSDIVVLLRLYDNLRFLYENCLWSVSFHEFHQYIRNSMSLLIEKAEYERTRDIDELGFSFFGKKSGFFMEYYDFVNISRHFKIDDIKNLERSCSIDKIRFGEQEKIEEYLVGIAEEITKQFSANGMNVVFYTQFISEAKAALYFAKYVKLSEEGLGKIVKALLFYFPERDLDIGKRYVWLERLTKCNELPKSIISIIDDFLVLQAEKHIDQNYSEVSSNGLYSRDYGALIKHFEKNFISKRLSEITLCLTQDKQKQIDFLFKLLPLLSTNAKSHLLSFKSVENINDLMNGIRIGLIDEFTPEHEELIIEYLETRKVNYIVEKEKGIQTFSSNDYMSTFGIWYFLEEINNSKMEEFIGMDDQYDFFVDPENFDYKKFIPSWLKNYNDKLLGKIAGNKHMKHHVIEVLKERVKNSNDKRYLEILMNYFI

来源 Source

来源生物 organism	Bacillus subtilis
NCBI 分类编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli B

Entity 2 polymer

描述 description	DSR anti-defence 1
分子量 formula_weight	13872.9 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	C,F

MIEIFKDTGATHDLVYHSKINTFVWDVEFDIVLSDSKELNKCYFVKCFNPYRINGKCDFAVSSIDIFSEGKRLLIENEFNFKITKAVHVATSKDVTEIVLHLSERISSPFPIVKEVVYLD

来源 Source

来源生物 organism	Bacillus subtilis
NCBI 分类编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli B

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7. 引用文献 (1)

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分辨率 resolution	3.33 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	91205

fit	/app/data/saxs_computation/y3/8y3y/8y3y.fit
pddf	/app/data/pr_computation/y3/8y3y/8y3y.pr.out
profile	/app/data/saxs_computation/y3/8y3y/8y3y.dat

The Cryo-EM structure of anti-phage defense associated DSR2 tetramer bound with two DSAD1 inhibitors (opposite side)

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 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)