SAXSdb — 2f8t

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2f8t
沉积日期 deposition_date	2005-12-03
结构标题 title	Crystal structure of Aa-Ago with externally-bound siRNA
关键词 keywords	Argonaute, siRNA, RISC loading complex, RNA BINDING PROTEIN-RNA COMPLEX; RNA BINDING PROTEIN/RNA
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	45.62 Å
回转半径 Rg (电子) rg_electron	43.62 Å
零角强度 I(0) i0	492687000.00
分子量 molecular_weight	182070.0 kDa
排除体积 excluded_volume	228250 Å³
包络体积 envelope_volume	323550 Å³
水化壳体积 shell_volume	63553 Å³
包络直径 envelope_diameter	171.8 Å
壳层 Rg shell_rg	46.92 Å
包络 Rg envelope_rg	43.53 Å
形状 Rg shape_rg	43.48 Å
总 Rg total_rg	44.27 Å
总原子数 total_atoms	12790
残基数 n_residues	1458
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	166.0 Å
Rg (实空间) rg_real	45.88 Å
Rg 误差 (实空间) rg_real_error	1.60 Å
I(0) (实空间) i0_real	4.9270e+08
I(0) 误差 (实空间) i0_real_error	9.6740e+06
Rg (倒空间) rg_reciprocal	45.62 Å
I(0) (倒空间) i0_reciprocal	492500000.0000
解质量估计 total_estimate	0.8432
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	47.4 Å
偏度 Skewness skewness	0.490
峰度 Kurtosis kurtosis	-0.139
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	43140000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.733; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.843; Smooth: 0.916

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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	26-MER
分子量 formula_weight	8281.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	C,D
原子数 atom_count	12841

AGACAGCAUGCAUGCAUGCUGUCUUU

Entity 2 polymer

描述 description	Argonaute protein
分子量 formula_weight	83264.4 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

MGKEALLNLYRIEYRPKDTTFTVFKPTHEIQKEKLNKVRWRVFLQTGLPTFRREDEFWCAGKVEKDTLYLTLSNGEIVELKRVGEEEFRGFQNERECQELFRDFLTKTKVKDKFISDFYKKFRDKITVQGKNRKIALIPEVNEKVLKSEEGYFLLHLDLKFRIQPFETLQTLLERNDFNPKRIRVKPIGIDFVGRVQDVFKAKEKGEEFFRLCMERSTHKSSKKAWEELLKNRELREKAFLVVLEKGYTYPATILKPVLTYENLEDEERNEVADIVRMEPGKRLNLIRYILRRYVKALRDYGWYISPEEERAKGKLNFKDTVLDAKGKNTKVITNLRKFLELCRPFVKKDVLSVEIISVSVYKKLEWRKEEFLKELINFLKNKGIKLKIKGKSLILAQTREEAKEKLIPVINKIKDVDLVIVFLEEYPKVDPYKSFLLYDFVKRELLKKMIPSQVILNRTLKNENLKFVLLNVAEQVLAKTGNIPYKLKEIEGKVDAFVGIDISRITRDGKTVNAVAFTKIFNSKGELVRYYLTSYPAFGEKLTEKAIGDVFSLLEKLGFKKGSKIVVHRDGRLYRDEVAAFKKYGELYGYSLELLEIIKRNNPRFFSNEKFIKGYFYKLSEDSVILATYNQVYEGTHQPIKVRKVYGELPVEVLCSQILSLTLMNYSSFQPIKLPATVHYSDKITKLMLRGIEPIKKEGDIMYWL

来源 Source

来源生物 organism	Aquifex aeolicus
NCBI 分类编号 ncbi_taxonomy_id	63363
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 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	51

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d2f8ta1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.14 — PAZ domain
家族 Family family	b.34.14.1 — PAZ domain

结构域编号 domain_id	d2f8ta3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.44 — Phosphotyrosine protein phosphatases I-like
超家族 Superfamily superfamily	c.44.3 — PIWI domain N-terminal-like
家族 Family family	c.44.3.1 — PIWI domain N-terminal

结构域编号 domain_id	d2f8ta4
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.3 — Ribonuclease H-like
家族 Family family	c.55.3.15 — PIWI domain C-terminal

结构域编号 domain_id	d2f8tb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.14 — PAZ domain
家族 Family family	b.34.14.1 — PAZ domain

结构域编号 domain_id	d2f8tb3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.44 — Phosphotyrosine protein phosphatases I-like
超家族 Superfamily superfamily	c.44.3 — PIWI domain N-terminal-like
家族 Family family	c.44.3.1 — PIWI domain N-terminal

结构域编号 domain_id	d2f8tb4
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.3 — Ribonuclease H-like
家族 Family family	c.55.3.15 — PIWI domain C-terminal

CATH v4.4 (6 domains)

结构域编号 domain_id	2f8tA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	340 — PAZ domain fold
同源超家族 H-superfamily homologous superfamily	10 — PAZ domain superfamily

结构域编号 domain_id	2f8tA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

结构域编号 domain_id	2f8tA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

结构域编号 domain_id	2f8tB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	340 — PAZ domain fold
同源超家族 H-superfamily homologous superfamily	10 — PAZ domain superfamily

结构域编号 domain_id	2f8tB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

结构域编号 domain_id	2f8tB04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

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7. 引用文献 (1)

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晶胞边长 a length_a	81.200 Å
晶胞边长 b length_b	118.077 Å
晶胞边长 c length_c	98.498 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	99.57 °
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	—

分辨率 resolution	3.100 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.2087
R_work r_work	0.2040
R_free r_free	0.2969

fit	/app/data/saxs_computation/f8/2f8t/2f8t.fit
pddf	/app/data/pr_computation/f8/2f8t/2f8t.pr.out
profile	/app/data/saxs_computation/f8/2f8t/2f8t.dat

Crystal structure of Aa-Ago with externally-bound siRNA

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 (3)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 water

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)