SAXSdb — 1ihm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ihm
沉积日期 deposition_date	2001-04-19
结构标题 title	CRYSTAL STRUCTURE ANALYSIS OF NORWALK VIRUS CAPSID
关键词 keywords	Beta-barrel, EF-Tu-LIKE domain caliciviridae, T=3 icosahedral capsid, Icosahedral virus, Virus; VIRUS
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	35.97 Å
回转半径 Rg (电子) rg_electron	34.91 Å
零角强度 I(0) i0	385732000.00
分子量 molecular_weight	159950.0 kDa
排除体积 excluded_volume	200410 Å³
包络体积 envelope_volume	259240 Å³
水化壳体积 shell_volume	59374 Å³
包络直径 envelope_diameter	117.8 Å
壳层 Rg shell_rg	43.38 Å
包络 Rg envelope_rg	34.47 Å
形状 Rg shape_rg	34.91 Å
总 Rg total_rg	35.50 Å
总原子数 total_atoms	11284
残基数 n_residues	1495
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	109.2 Å
Rg (实空间) rg_real	35.71 Å
Rg 误差 (实空间) rg_real_error	0.70 Å
I(0) (实空间) i0_real	3.8570e+08
I(0) 误差 (实空间) i0_real_error	6.5830e+06
Rg (倒空间) rg_reciprocal	35.88 Å
I(0) (倒空间) i0_reciprocal	385800000.0000
解质量估计 total_estimate	0.9021
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	49.6 Å
偏度 Skewness skewness	0.034
峰度 Kurtosis kurtosis	-0.561
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	90420000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.957

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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)

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1ihma_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
超家族 Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
家族 Family family	b.121.4.3 — Caliciviridae-like VP

结构域编号 domain_id	d1ihmb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
超家族 Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
家族 Family family	b.121.4.3 — Caliciviridae-like VP

结构域编号 domain_id	d1ihmc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
超家族 Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
家族 Family family	b.121.4.3 — Caliciviridae-like VP

CATH v4.4 (9 domains)

结构域编号 domain_id	1ihmA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1ihmA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	510 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
同源超家族 H-superfamily homologous superfamily	10 — Positive stranded ssRNA viruses

结构域编号 domain_id	1ihmA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	120 — Positive stranded ssRNA viruses

结构域编号 domain_id	1ihmB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1ihmB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	510 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
同源超家族 H-superfamily homologous superfamily	10 — Positive stranded ssRNA viruses

结构域编号 domain_id	1ihmB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	120 — Positive stranded ssRNA viruses

结构域编号 domain_id	1ihmC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1ihmC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	510 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
同源超家族 H-superfamily homologous superfamily	10 — Positive stranded ssRNA viruses

结构域编号 domain_id	1ihmC03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	120 — Positive stranded ssRNA viruses

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7. 引用文献 (1)

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晶胞边长 a length_a	605.740 Å
晶胞边长 b length_b	605.740 Å
晶胞边长 c length_c	466.710 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	720

空间群 space_group	P 42 21 2
空间群编号 int_tables_number	94
晶系 crystal_system	—

分辨率 resolution	3.400 Å
最低分辨率 resolution_low	35.000 Å
R 因子 r_factor	0.2600
R_work r_work	—
R_free r_free	—

描述 description	capsid protein
分子量 formula_weight	56629.8 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	11284

CRYSTAL STRUCTURE ANALYSIS OF NORWALK VIRUS CAPSID

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

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Norwalk virus
NCBI 分类编号 ncbi_taxonomy_id	11983
宿主生物 host_organism	Spodoptera frugiperda

fit	/app/data/saxs_computation/ih/1ihm/1ihm.fit
pddf	/app/data/pr_computation/ih/1ihm/1ihm.pr.out
profile	/app/data/saxs_computation/ih/1ihm/1ihm.dat