1pfi

PF1 VIRUS STRUCTURE: HELICAL COAT PROTEIN AND DNA WITH PARAXIAL PHOSPHATES

Method: FIBER DIFFRACTION D_max: 78.7 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	1pfi
沉积日期 deposition_date	1994-04-06
结构标题 title	PF1 VIRUS STRUCTURE: HELICAL COAT PROTEIN AND DNA WITH PARAXIAL PHOSPHATES
关键词 keywords	COMPLEX(VIRAL COAT PROTEIN-DNA), Helical virus, Virus; VIRUS
实验方法 method	FIBER DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	24.99 Å
回转半径 Rg (电子) rg_electron	24.12 Å
零角强度 I(0) i0	1848710.00
分子量 molecular_weight	9797.0 kDa
排除体积 excluded_volume	12344 Å³
包络体积 envelope_volume	20147 Å³
水化壳体积 shell_volume	8173 Å³
包络直径 envelope_diameter	79.8 Å
壳层 Rg shell_rg	27.42 Å
包络 Rg envelope_rg	23.39 Å
形状 Rg shape_rg	24.08 Å
总 Rg total_rg	24.86 Å
总原子数 total_atoms	1392
残基数 n_residues	93
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	78.7 Å
Rg (实空间) rg_real	25.22 Å
Rg 误差 (实空间) rg_real_error	0.72 Å
I(0) (实空间) i0_real	1.8490e+06
I(0) 误差 (实空间) i0_real_error	2.7450e+04
Rg (倒空间) rg_reciprocal	25.17 Å
I(0) (倒空间) i0_reciprocal	1849000.0000
解质量估计 total_estimate	0.8090
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	32.5 Å
偏度 Skewness skewness	0.204
峰度 Kurtosis kurtosis	-0.728
角度范围 angular_range	— – 0.3200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	54660.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.640; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.641; Smooth: 0.954

▶

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

▶

5. 实体与聚合体信息 (2)

Entity 1 polymer

描述 description	MAJOR COAT PROTEIN OF PF1 VIRUS
分子量 formula_weight	4612.4 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	1392

GVIDTSAVESAITDGQGDMKAIGGYIVGALVILAVAGLIYSMLRKA

来源 Source

来源生物 organism	Pseudomonas phage Pf1
NCBI 分类编号 ncbi_taxonomy_id	10871

Entity 2 polymer

描述 description	;DNA (5'-D(P*C)-3') ;
分子量 formula_weight	307.2 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	C,D

来源 Source

来源生物 organism	Pseudomonas phage Pf1
NCBI 分类编号 ncbi_taxonomy_id	10871

▼

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1pfia_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.4 — Inovirus (filamentous phage) major coat protein
家族 Family family	h.1.4.1 — Inovirus (filamentous phage) major coat protein

结构域编号 domain_id	d1pfib_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.4 — Inovirus (filamentous phage) major coat protein
家族 Family family	h.1.4.1 — Inovirus (filamentous phage) major coat protein

CATH v4.4 (2 domains)

结构域编号 domain_id	1pfiA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	1pfiB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	230 —

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	1

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

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/pf/1pfi/1pfi.fit
pddf	/app/data/pr_computation/pf/1pfi/1pfi.pr.out
profile	/app/data/saxs_computation/pf/1pfi/1pfi.dat

PF1 VIRUS STRUCTURE: HELICAL COAT PROTEIN AND DNA WITH PARAXIAL PHOSPHATES

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

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)