1knz

;Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer ;

Method: X-RAY DIFFRACTION D_max: 155.8 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	1knz
沉积日期 deposition_date	2001-12-19
结构标题 title	;Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer ;
关键词 keywords	Protein-ssRNA complex, Viral protein-RNA COMPLEX; Viral 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	45.85 Å
回转半径 Rg (电子) rg_electron	46.54 Å
零角强度 I(0) i0	283920000.00
分子量 molecular_weight	128350.0 kDa
排除体积 excluded_volume	156880 Å³
包络体积 envelope_volume	241110 Å³
水化壳体积 shell_volume	47567 Å³
包络直径 envelope_diameter	158.1 Å
壳层 Rg shell_rg	45.43 Å
包络 Rg envelope_rg	44.80 Å
形状 Rg shape_rg	46.58 Å
总 Rg total_rg	46.35 Å
总原子数 total_atoms	8950
残基数 n_residues	1188
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	155.8 Å
Rg (实空间) rg_real	46.20 Å
Rg 误差 (实空间) rg_real_error	1.69 Å
I(0) (实空间) i0_real	2.8390e+08
I(0) 误差 (实空间) i0_real_error	5.0690e+06
Rg (倒空间) rg_reciprocal	45.86 Å
I(0) (倒空间) i0_reciprocal	283800000.0000
解质量估计 total_estimate	0.8358
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	50.4 Å
偏度 Skewness skewness	0.418
峰度 Kurtosis kurtosis	-0.479
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6049000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.755; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.655

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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	5'-R(UPGPAPCP*C)-3'
分子量 formula_weight	1546.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	W,X,Y,Z
原子数 atom_count	9555

UGACC

Entity 2 polymer

描述 description	Nonstructural RNA-binding Protein 34
分子量 formula_weight	18380.0 kDa
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,I,J,M,N

LGSMESTQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALNNKFGSAIRNRNWLADTSRPAKLDEDVNKLRMMLSSKGIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVEVDDSFVDEKME

来源 Source

来源生物 organism	Simian rotavirus A/SA11
NCBI 分类编号 ncbi_taxonomy_id	10923
宿主生物 host_organism	Escherichia coli

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	605

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6. 折叠分类 (SCOP + CATH) 28 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1knza_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.34 — NSP3 homodimer
超家族 Superfamily superfamily	e.34.1 — NSP3 homodimer
家族 Family family	e.34.1.1 — NSP3 homodimer

结构域编号 domain_id	d1knzb1
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.34 — NSP3 homodimer
超家族 Superfamily superfamily	e.34.1 — NSP3 homodimer
家族 Family family	e.34.1.1 — NSP3 homodimer

结构域编号 domain_id	d1knzb2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1knzc_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.34 — NSP3 homodimer
超家族 Superfamily superfamily	e.34.1 — NSP3 homodimer
家族 Family family	e.34.1.1 — NSP3 homodimer

结构域编号 domain_id	d1knzd1
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.34 — NSP3 homodimer
超家族 Superfamily superfamily	e.34.1 — NSP3 homodimer
家族 Family family	e.34.1.1 — NSP3 homodimer

结构域编号 domain_id	d1knzd2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1knzi_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.34 — NSP3 homodimer
超家族 Superfamily superfamily	e.34.1 — NSP3 homodimer
家族 Family family	e.34.1.1 — NSP3 homodimer

结构域编号 domain_id	d1knzj1
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.34 — NSP3 homodimer
超家族 Superfamily superfamily	e.34.1 — NSP3 homodimer
家族 Family family	e.34.1.1 — NSP3 homodimer

结构域编号 domain_id	d1knzj2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1knzm_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.34 — NSP3 homodimer
超家族 Superfamily superfamily	e.34.1 — NSP3 homodimer
家族 Family family	e.34.1.1 — NSP3 homodimer

结构域编号 domain_id	d1knzn1
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.34 — NSP3 homodimer
超家族 Superfamily superfamily	e.34.1 — NSP3 homodimer
家族 Family family	e.34.1.1 — NSP3 homodimer

结构域编号 domain_id	d1knzn2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (16 domains)

结构域编号 domain_id	1knzA01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	20 — Rotavirus non-structural protein NSP3, N-terminal domain

结构域编号 domain_id	1knzA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1610 —

结构域编号 domain_id	1knzB01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	20 — Rotavirus non-structural protein NSP3, N-terminal domain

结构域编号 domain_id	1knzB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1610 —

结构域编号 domain_id	1knzC01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	20 — Rotavirus non-structural protein NSP3, N-terminal domain

结构域编号 domain_id	1knzC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1610 —

结构域编号 domain_id	1knzD01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	20 — Rotavirus non-structural protein NSP3, N-terminal domain

结构域编号 domain_id	1knzD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1610 —

结构域编号 domain_id	1knzI01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	20 — Rotavirus non-structural protein NSP3, N-terminal domain

结构域编号 domain_id	1knzI02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1610 —

结构域编号 domain_id	1knzJ01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	20 — Rotavirus non-structural protein NSP3, N-terminal domain

结构域编号 domain_id	1knzJ02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1610 —

结构域编号 domain_id	1knzM01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	20 — Rotavirus non-structural protein NSP3, N-terminal domain

结构域编号 domain_id	1knzM02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1610 —

结构域编号 domain_id	1knzN01
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	20 — Rotavirus non-structural protein NSP3, N-terminal domain

结构域编号 domain_id	1knzN02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1610 —

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7. 引用文献 (1)

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晶胞边长 a length_a	40.275 Å
晶胞边长 b length_b	85.359 Å
晶胞边长 c length_c	96.051 Å
晶胞夹角 α angle_alpha	89.99 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.05 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.450 Å
最低分辨率 resolution_low	22.000 Å
R 因子 r_factor	—
R_work r_work	0.2280
R_free r_free	0.2800

fit	/app/data/saxs_computation/kn/1knz/1knz.fit
pddf	/app/data/pr_computation/kn/1knz/1knz.pr.out
profile	/app/data/saxs_computation/kn/1knz/1knz.dat

;Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer ;

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) 28 domains

SCOP 2.08 (12 domains)

CATH v4.4 (16 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)