1sfk

Core (C) protein from West Nile Virus, subtype Kunjin

Method: X-RAY DIFFRACTION D_max: 86.7 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1sfk
沉积日期 deposition_date	2004-02-19
结构标题 title	Core (C) protein from West Nile Virus, subtype Kunjin
关键词 keywords	ALPHA HELIX, Viral protein; VIRAL PROTEIN
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	27.08 Å
回转半径 Rg (电子) rg_electron	26.12 Å
零角强度 I(0) i0	58028200.00
分子量 molecular_weight	62968.0 kDa
排除体积 excluded_volume	80829 Å³
包络体积 envelope_volume	102720 Å³
水化壳体积 shell_volume	32506 Å³
包络直径 envelope_diameter	93.7 Å
壳层 Rg shell_rg	33.78 Å
包络 Rg envelope_rg	25.99 Å
形状 Rg shape_rg	26.04 Å
总 Rg total_rg	27.30 Å
总原子数 total_atoms	4421
残基数 n_residues	553
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	86.7 Å
Rg (实空间) rg_real	26.92 Å
Rg 误差 (实空间) rg_real_error	0.66 Å
I(0) (实空间) i0_real	5.8030e+07
I(0) 误差 (实空间) i0_real_error	8.0010e+05
Rg (倒空间) rg_reciprocal	26.97 Å
I(0) (倒空间) i0_reciprocal	58030000.0000
解质量估计 total_estimate	0.8119
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	36.8 Å
偏度 Skewness skewness	0.143
峰度 Kurtosis kurtosis	-0.360
角度范围 angular_range	— – 0.2950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15890000.0000
实空间数据点数 n_real_points	60
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.851; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (6)

Entity 1 polymer

描述 description	Core protein
分子量 formula_weight	8615.3 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,E,F,G,H
原子数 atom_count	4448

RVLSLTGLKRAMLSLIDGRGPTRFVLALLAFFRFTAIAPTRAVLDRWRSVNKQTAMKHLLSFKKELGTLTSAINRR

来源 Source

来源生物 organism	Kunjin virus
NCBI 分类编号 ncbi_taxonomy_id	11078
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	TETRAETHYLENE GLYCOL
分子量 formula_weight	194.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 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	27

▼

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1sfka_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.190 — Flavivirus capsid protein C
超家族 Superfamily superfamily	a.190.1 — Flavivirus capsid protein C
家族 Family family	a.190.1.1 — Flavivirus capsid protein C

结构域编号 domain_id	d1sfkb_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.190 — Flavivirus capsid protein C
超家族 Superfamily superfamily	a.190.1 — Flavivirus capsid protein C
家族 Family family	a.190.1.1 — Flavivirus capsid protein C

结构域编号 domain_id	d1sfkc_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.190 — Flavivirus capsid protein C
超家族 Superfamily superfamily	a.190.1 — Flavivirus capsid protein C
家族 Family family	a.190.1.1 — Flavivirus capsid protein C

结构域编号 domain_id	d1sfkd_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.190 — Flavivirus capsid protein C
超家族 Superfamily superfamily	a.190.1 — Flavivirus capsid protein C
家族 Family family	a.190.1.1 — Flavivirus capsid protein C

结构域编号 domain_id	d1sfke_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.190 — Flavivirus capsid protein C
超家族 Superfamily superfamily	a.190.1 — Flavivirus capsid protein C
家族 Family family	a.190.1.1 — Flavivirus capsid protein C

结构域编号 domain_id	d1sfkf_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.190 — Flavivirus capsid protein C
超家族 Superfamily superfamily	a.190.1 — Flavivirus capsid protein C
家族 Family family	a.190.1.1 — Flavivirus capsid protein C

结构域编号 domain_id	d1sfkg_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.190 — Flavivirus capsid protein C
超家族 Superfamily superfamily	a.190.1 — Flavivirus capsid protein C
家族 Family family	a.190.1.1 — Flavivirus capsid protein C

结构域编号 domain_id	d1sfkh_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.190 — Flavivirus capsid protein C
超家族 Superfamily superfamily	a.190.1 — Flavivirus capsid protein C
家族 Family family	a.190.1.1 — Flavivirus capsid protein C

CATH v4.4 (8 domains)

结构域编号 domain_id	1sfkA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	930 —

结构域编号 domain_id	1sfkB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	930 —

结构域编号 domain_id	1sfkC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	930 —

结构域编号 domain_id	1sfkD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	930 —

结构域编号 domain_id	1sfkE00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	930 —

结构域编号 domain_id	1sfkF00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	930 —

结构域编号 domain_id	1sfkG00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	930 —

结构域编号 domain_id	1sfkH00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	930 —

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	85.655 Å
晶胞边长 b length_b	85.655 Å
晶胞边长 c length_c	214.384 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	64

空间群 space_group	I 41
空间群编号 int_tables_number	80
晶系 crystal_system	—

分辨率 resolution	3.200 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.2521
R_work r_work	0.2491
R_free r_free	0.3112

fit	/app/data/saxs_computation/sf/1sfk/1sfk.fit
pddf	/app/data/pr_computation/sf/1sfk/1sfk.pr.out
profile	/app/data/saxs_computation/sf/1sfk/1sfk.dat

Core (C) protein from West Nile Virus, subtype Kunjin

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 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)