1noh

The structure of bacteriophage phi29 scaffolding protein gp7 after prohead assembly

Method: X-RAY DIFFRACTION D_max: 96.8 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	1noh
沉积日期 deposition_date	2003-01-16
结构标题 title	The structure of bacteriophage phi29 scaffolding protein gp7 after prohead assembly
关键词 keywords	coiled-coil, 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	31.51 Å
回转半径 Rg (电子) rg_electron	30.95 Å
零角强度 I(0) i0	18438300.00
分子量 molecular_weight	33381.0 kDa
排除体积 excluded_volume	41778 Å³
包络体积 envelope_volume	58309 Å³
水化壳体积 shell_volume	16840 Å³
包络直径 envelope_diameter	97.5 Å
壳层 Rg shell_rg	35.87 Å
包络 Rg envelope_rg	29.84 Å
形状 Rg shape_rg	30.93 Å
总 Rg total_rg	31.52 Å
总原子数 total_atoms	2356
残基数 n_residues	292
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	96.8 Å
Rg (实空间) rg_real	31.59 Å
Rg 误差 (实空间) rg_real_error	0.64 Å
I(0) (实空间) i0_real	1.8440e+07
I(0) 误差 (实空间) i0_real_error	2.5960e+05
Rg (倒空间) rg_reciprocal	31.56 Å
I(0) (倒空间) i0_reciprocal	18440000.0000
解质量估计 total_estimate	0.7826
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	17.4 Å
偏度 Skewness skewness	0.058
峰度 Kurtosis kurtosis	-1.083
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	983400.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.559; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.582; Smooth: 0.912

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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 (1)

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1noha_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.24 — Head morphogenesis protein gp7
家族 Family family	h.1.24.1 — Head morphogenesis protein gp7

结构域编号 domain_id	d1nohb_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.24 — Head morphogenesis protein gp7
家族 Family family	h.1.24.1 — Head morphogenesis protein gp7

结构域编号 domain_id	d1nohc_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.24 — Head morphogenesis protein gp7
家族 Family family	h.1.24.1 — Head morphogenesis protein gp7

结构域编号 domain_id	d1nohd_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.24 — Head morphogenesis protein gp7
家族 Family family	h.1.24.1 — Head morphogenesis protein gp7

CATH v4.4 (4 domains)

结构域编号 domain_id	1nohA00
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	400 —

结构域编号 domain_id	1nohB00
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	400 —

结构域编号 domain_id	1nohC00
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	400 —

结构域编号 domain_id	1nohD00
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	400 —

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7. 引用文献 (1)

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晶胞边长 a length_a	114.005 Å
晶胞边长 b length_b	117.301 Å
晶胞边长 c length_c	105.933 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	32

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	36.150 Å
R 因子 r_factor	0.2540
R_work r_work	0.2540
R_free r_free	0.2900

描述 description	HEAD MORPHOGENESIS PROTEIN
分子量 formula_weight	11165.4 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	2356

The structure of bacteriophage phi29 scaffolding protein gp7 after prohead assembly

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 (1)

Entity 1 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Bacillus phage phi29
NCBI 分类编号 ncbi_taxonomy_id	10756
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/no/1noh/1noh.fit
pddf	/app/data/pr_computation/no/1noh/1noh.pr.out
profile	/app/data/saxs_computation/no/1noh/1noh.dat