SAXSdb — 1ohf

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ohf
沉积日期 deposition_date	2003-05-26
结构标题 title	The refined structure of Nudaurelia capensis omega virus
关键词 keywords	VIRUS, VIRAL COAT, AUTO-CATALYTIC CLEAVAGE, QUASIEQUIVALENCE, NWV, ICOSAHEDRAL 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	38.15 Å
回转半径 Rg (电子) rg_electron	37.35 Å
零角强度 I(0) i0	895113000.00
分子量 molecular_weight	245500.0 kDa
排除体积 excluded_volume	306750 Å³
包络体积 envelope_volume	374930 Å³
水化壳体积 shell_volume	77962 Å³
包络直径 envelope_diameter	123.4 Å
壳层 Rg shell_rg	47.14 Å
包络 Rg envelope_rg	37.35 Å
形状 Rg shape_rg	37.32 Å
总 Rg total_rg	37.95 Å
总原子数 total_atoms	17335
残基数 n_residues	2263
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	117.2 Å
Rg (实空间) rg_real	37.87 Å
Rg 误差 (实空间) rg_real_error	0.65 Å
I(0) (实空间) i0_real	8.9510e+08
I(0) 误差 (实空间) i0_real_error	1.3350e+07
Rg (倒空间) rg_reciprocal	38.05 Å
I(0) (倒空间) i0_reciprocal	895300000.0000
解质量估计 total_estimate	0.8874
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	0
主峰位置 r_peak_primary	— Å
偏度 Skewness skewness	0.134
峰度 Kurtosis kurtosis	-0.438
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	292300000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.857

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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 (4)

Entity 1 polymer

描述 description	p70
分子量 formula_weight	62094.8 kDa
来源方法 src_method	nat
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,C,D
原子数 atom_count	17851

MDSNSASGKRRSRNVRIAANTVNVAPKQRQARGRRARSRANNIDNVTAAAQELGQSLDANVITFPTNVATMPEFRSWARGKLDIDQDSIGWYFKYLDPAGATESARAVGEYSKIPDGLVKFSVDAEIREIYNEECPTVSDASIPLDGAQWSLSIISYPMFRTAYFAVANVDNKEISLDVTNDLIVWLNNLASWRDVVDSGQWFTFSDDPTWFVRIRVLHPTYDLPDPTEGLLRTVSDYRLTYKSITCEANMPTLVDQGFWIGGHYALTPIATTQNAVEGSGFVHPFNVTRPGIAAGVTLTWASMPPGGSAPSGDPAWIPDSTTQFQWRHGGFDAPTGVITYTIPRGYTMQYFDTTTNEWNGFANPDDVVTFGQTGGAAGTNATITITAPTVTLTILATTTSAANVINFRNLDAETTAASNRSEVPLPPLTFGQTAPNNPKIEQTLVKDTLGSYLVHSKMRNPVFQLTPASSFGAISFTNPGFDRNLDLPGFGGIRDSLDVNMSTAVCHFRSLSKSCSIVTKTYQGWEGVTNVNTPFGQFAHSGLLKNDEILCLADDLATRLTGVYGATDN

Entity 2 polymer

描述 description	p70
分子量 formula_weight	7815.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E,F,G,H

FAAAVLAFAANMLTSVLKSEATTSVIKELGNQATGLANQGLARLPGLLASIPGKIAARVRARRDRRRAARMNNN

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	4

Entity 4 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	516

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1ohfa_
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.121.4.8 — Tetraviridae-like VP

结构域编号 domain_id	d1ohfb_
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.121.4.8 — Tetraviridae-like VP

结构域编号 domain_id	d1ohfc_
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.121.4.8 — Tetraviridae-like VP

结构域编号 domain_id	d1ohfd_
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.121.4.8 — Tetraviridae-like VP

CATH v4.4 (8 domains)

结构域编号 domain_id	1ohfA02
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	1ohfA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	270 — Mutm (Fpg) Protein; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	70 —

结构域编号 domain_id	1ohfB02
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	1ohfB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	270 — Mutm (Fpg) Protein; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	70 —

结构域编号 domain_id	1ohfC02
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	1ohfC03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	270 — Mutm (Fpg) Protein; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	70 —

结构域编号 domain_id	1ohfD02
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	1ohfD03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	270 — Mutm (Fpg) Protein; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	70 —

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7. 引用文献 (3)

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晶胞边长 a length_a	413.550 Å
晶胞边长 b length_b	410.220 Å
晶胞边长 c length_c	419.670 Å
晶胞夹角 α angle_alpha	59.13 °
晶胞夹角 β angle_beta	58.90 °
晶胞夹角 γ angle_gamma	64.04 °
晶胞分子数 Z z_pdb	240

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

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2210

fit	/app/data/saxs_computation/oh/1ohf/1ohf.fit
pddf	/app/data/pr_computation/oh/1ohf/1ohf.pr.out
profile	/app/data/saxs_computation/oh/1ohf/1ohf.dat

The refined structure of Nudaurelia capensis omega virus

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 (4)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)