SAXSdb — 1vps

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1vps
沉积日期 deposition_date	1997-03-07
结构标题 title	POLYOMAVIRUS VP1 PENTAMER COMPLEXED WITH A DISIALYLATED HEXASACCHARIDE
关键词 keywords	VIRUS COAT PROTEIN, OLIGOSACCHARIDE BINDING, VIRUS ASSEMBLY, SIALIC ACID, Viral protein; VIRAL PROTEIN
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	34.63 Å
回转半径 Rg (电子) rg_electron	33.53 Å
零角强度 I(0) i0	411570000.00
分子量 molecular_weight	163110.0 kDa
排除体积 excluded_volume	203790 Å³
包络体积 envelope_volume	258690 Å³
水化壳体积 shell_volume	59968 Å³
包络直径 envelope_diameter	105.3 Å
壳层 Rg shell_rg	43.26 Å
包络 Rg envelope_rg	33.41 Å
形状 Rg shape_rg	33.46 Å
总 Rg total_rg	34.45 Å
总原子数 total_atoms	11464
残基数 n_residues	1429
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	103.1 Å
Rg (实空间) rg_real	34.37 Å
Rg 误差 (实空间) rg_real_error	0.54 Å
I(0) (实空间) i0_real	4.1160e+08
I(0) 误差 (实空间) i0_real_error	6.3890e+06
Rg (倒空间) rg_reciprocal	34.53 Å
I(0) (倒空间) i0_reciprocal	411600000.0000
解质量估计 total_estimate	0.8973
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	49.3 Å
偏度 Skewness skewness	0.003
峰度 Kurtosis kurtosis	-0.540
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	117500000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.910

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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	POLYOMAVIRUS VP1 PENTAMER
分子量 formula_weight	32087.2 kDa
来源方法 src_method	man
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E
原子数 atom_count	13591

GGMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPGNNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVKNPYP

来源 Source

来源生物 organism	Murine polyomavirus
NCBI 分类编号 ncbi_taxonomy_id	10634
宿主生物 host_organism	Escherichia coli

Entity 2 branched

描述 description	;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	965.9 kDa
来源方法 src_method	man
拷贝数 entity_count	5

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	2127

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d1vpsa_
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.121.6 — Group I dsDNA viruses
家族 Family family	b.121.6.1 — Papovaviridae-like VP

结构域编号 domain_id	d1vpsb_
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.121.6 — Group I dsDNA viruses
家族 Family family	b.121.6.1 — Papovaviridae-like VP

结构域编号 domain_id	d1vpsc_
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.121.6 — Group I dsDNA viruses
家族 Family family	b.121.6.1 — Papovaviridae-like VP

结构域编号 domain_id	d1vpsd_
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.121.6 — Group I dsDNA viruses
家族 Family family	b.121.6.1 — Papovaviridae-like VP

结构域编号 domain_id	d1vpse_
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.121.6 — Group I dsDNA viruses
家族 Family family	b.121.6.1 — Papovaviridae-like VP

CATH v4.4 (5 domains)

结构域编号 domain_id	1vpsA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	175 — Polyomavirus Vp1; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Capsid protein VP1,Polyomavirus

结构域编号 domain_id	1vpsB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	175 — Polyomavirus Vp1; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Capsid protein VP1,Polyomavirus

结构域编号 domain_id	1vpsC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	175 — Polyomavirus Vp1; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Capsid protein VP1,Polyomavirus

结构域编号 domain_id	1vpsD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	175 — Polyomavirus Vp1; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Capsid protein VP1,Polyomavirus

结构域编号 domain_id	1vpsE00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	175 — Polyomavirus Vp1; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Capsid protein VP1,Polyomavirus

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7. 引用文献 (4)

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晶胞边长 a length_a	221.500 Å
晶胞边长 b length_b	221.500 Å
晶胞边长 c length_c	99.800 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	120.00 °
晶胞分子数 Z z_pdb	30

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1770
R_work r_work	0.1770
R_free r_free	0.2050

fit	/app/data/saxs_computation/vp/1vps/1vps.fit
pddf	/app/data/pr_computation/vp/1vps/1vps.pr.out
profile	/app/data/saxs_computation/vp/1vps/1vps.dat

POLYOMAVIRUS VP1 PENTAMER COMPLEXED WITH A DISIALYLATED HEXASACCHARIDE

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