2gic

Crystal Structure of a vesicular stomatitis virus nucleocapsid-RNA complex

Method: X-RAY DIFFRACTION D_max: 158.7 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	2gic
沉积日期 deposition_date	2006-03-28
结构标题 title	Crystal Structure of a vesicular stomatitis virus nucleocapsid-RNA complex
关键词 keywords	nucleocapsid, protein-rna complex, negative strand virus, VIRUS-VIRAL PROTEIN-RNA COMPLEX; VIRUS/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	47.37 Å
回转半径 Rg (电子) rg_electron	47.55 Å
零角强度 I(0) i0	1012570000.00
分子量 molecular_weight	252080.0 kDa
排除体积 excluded_volume	308820 Å³
包络体积 envelope_volume	442850 Å³
水化壳体积 shell_volume	75793 Å³
包络直径 envelope_diameter	160.3 Å
壳层 Rg shell_rg	52.80 Å
包络 Rg envelope_rg	47.64 Å
形状 Rg shape_rg	47.54 Å
总 Rg total_rg	47.80 Å
总原子数 total_atoms	17432
残基数 n_residues	2131
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	158.7 Å
Rg (实空间) rg_real	47.46 Å
Rg 误差 (实空间) rg_real_error	1.68 Å
I(0) (实空间) i0_real	1.0130e+09
I(0) 误差 (实空间) i0_real_error	2.2090e+07
Rg (倒空间) rg_reciprocal	47.37 Å
I(0) (倒空间) i0_reciprocal	1012000000.0000
解质量估计 total_estimate	0.8789
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	48.1 Å
偏度 Skewness skewness	0.329
峰度 Kurtosis kurtosis	-0.570
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	225700000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.803

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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	45-MER
分子量 formula_weight	13732.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	R
原子数 atom_count	17432

UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU

Entity 2 polymer

描述 description	Nucleocapsid protein
分子量 formula_weight	47463.9 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

MSVTVKRIIDNTVIVPKLPANEDPVEYPADYFRKSKEIPLYINTTKSLSDLRGYVYQGLKSGNVSIIHVNSYLYGALKDIRGKLDKDWSSFGINIGKAGDTIGIFDLVSLKALDGVLPDGVSDASRTSADDKWLPLYLLGLYRVGRTQMPEYRKKLMDGLTNQCKMINEQFEPLVPEGRDIFDVWGNDSNYTKIVAAVDMFFHMFKKHECASFRYGTIVSRFKDCAALATFGHLCKITGMSTEDVTTWILNREVADEMVQMMLPGQEIDKADSYMPYLIDFGLSSKSPYSSVKNPAFHFWGQLTALLLRSTRARNARQPDDIEYTSLTTAGLLYAYAVGSSADLAQQFCVGDNKYTPDDSTGGLTTNAPPQGRDVVEWLGWFEDQNRKPTPDMMQYAKRAVMSLQGLREKTIGKYAKSEFDK

来源 Source

来源生物 organism	Vesicular stomatitis Indiana virus
NCBI 分类编号 ncbi_taxonomy_id	11277
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	URANYL (VI) ION
分子量 formula_weight	270.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	15

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6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d2gica1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.260 — Rhabdovirus nucleoprotein-like
超家族 Superfamily superfamily	a.260.1 — Rhabdovirus nucleoprotein-like
家族 Family family	a.260.1.1 — Rhabdovirus nucleocapsid protein

结构域编号 domain_id	d2gicb_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.260 — Rhabdovirus nucleoprotein-like
超家族 Superfamily superfamily	a.260.1 — Rhabdovirus nucleoprotein-like
家族 Family family	a.260.1.1 — Rhabdovirus nucleocapsid protein

结构域编号 domain_id	d2gicc_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.260 — Rhabdovirus nucleoprotein-like
超家族 Superfamily superfamily	a.260.1 — Rhabdovirus nucleoprotein-like
家族 Family family	a.260.1.1 — Rhabdovirus nucleocapsid protein

结构域编号 domain_id	d2gicd_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.260 — Rhabdovirus nucleoprotein-like
超家族 Superfamily superfamily	a.260.1 — Rhabdovirus nucleoprotein-like
家族 Family family	a.260.1.1 — Rhabdovirus nucleocapsid protein

结构域编号 domain_id	d2gice_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.260 — Rhabdovirus nucleoprotein-like
超家族 Superfamily superfamily	a.260.1 — Rhabdovirus nucleoprotein-like
家族 Family family	a.260.1.1 — Rhabdovirus nucleocapsid protein

CATH v4.4 (10 domains)

结构域编号 domain_id	2gicA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3570 — Rhabdovirus nucleoprotein-like fold
同源超家族 H-superfamily homologous superfamily	10 — Rhabdovirus nucleocapsid protein like domain

结构域编号 domain_id	2gicA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3610 — Rhabdovirus nucleoprotein-like
同源超家族 H-superfamily homologous superfamily	10 — Nucleoprotein

结构域编号 domain_id	2gicB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3570 — Rhabdovirus nucleoprotein-like fold
同源超家族 H-superfamily homologous superfamily	10 — Rhabdovirus nucleocapsid protein like domain

结构域编号 domain_id	2gicB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3610 — Rhabdovirus nucleoprotein-like
同源超家族 H-superfamily homologous superfamily	10 — Nucleoprotein

结构域编号 domain_id	2gicC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3570 — Rhabdovirus nucleoprotein-like fold
同源超家族 H-superfamily homologous superfamily	10 — Rhabdovirus nucleocapsid protein like domain

结构域编号 domain_id	2gicC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3610 — Rhabdovirus nucleoprotein-like
同源超家族 H-superfamily homologous superfamily	10 — Nucleoprotein

结构域编号 domain_id	2gicD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3570 — Rhabdovirus nucleoprotein-like fold
同源超家族 H-superfamily homologous superfamily	10 — Rhabdovirus nucleocapsid protein like domain

结构域编号 domain_id	2gicD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3610 — Rhabdovirus nucleoprotein-like
同源超家族 H-superfamily homologous superfamily	10 — Nucleoprotein

结构域编号 domain_id	2gicE01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3570 — Rhabdovirus nucleoprotein-like fold
同源超家族 H-superfamily homologous superfamily	10 — Rhabdovirus nucleocapsid protein like domain

结构域编号 domain_id	2gicE02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3610 — Rhabdovirus nucleoprotein-like
同源超家族 H-superfamily homologous superfamily	10 — Nucleoprotein

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7. 引用文献 (1)

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晶胞边长 a length_a	166.160 Å
晶胞边长 b length_b	236.316 Å
晶胞边长 c length_c	75.651 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	20

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.920 Å
最低分辨率 resolution_low	44.860 Å
R 因子 r_factor	0.2580
R_work r_work	0.2550
R_free r_free	0.3060

fit	/app/data/saxs_computation/gi/2gic/2gic.fit
pddf	/app/data/pr_computation/gi/2gic/2gic.pr.out
profile	/app/data/saxs_computation/gi/2gic/2gic.dat

Crystal Structure of a vesicular stomatitis virus nucleocapsid-RNA complex

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 non-polymer

6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (5 domains)

CATH v4.4 (10 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)