1ijg

Structure of the Bacteriophage phi29 Head-Tail Connector Protein

Method: X-RAY DIFFRACTION D_max: 144.2 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	1ijg
沉积日期 deposition_date	2001-04-26
结构标题 title	Structure of the Bacteriophage phi29 Head-Tail Connector Protein
关键词 keywords	alpha-helical bundle, RNA binding motif, 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	51.42 Å
回转半径 Rg (电子) rg_electron	50.76 Å
零角强度 I(0) i0	1735780000.00
分子量 molecular_weight	356910.0 kDa
排除体积 excluded_volume	449260 Å³
包络体积 envelope_volume	627660 Å³
水化壳体积 shell_volume	99546 Å³
包络直径 envelope_diameter	149.6 Å
壳层 Rg shell_rg	58.73 Å
包络 Rg envelope_rg	48.82 Å
形状 Rg shape_rg	50.75 Å
总 Rg total_rg	51.05 Å
总原子数 total_atoms	25224
残基数 n_residues	3084
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	144.2 Å
Rg (实空间) rg_real	51.17 Å
Rg 误差 (实空间) rg_real_error	0.88 Å
I(0) (实空间) i0_real	1.7360e+09
I(0) 误差 (实空间) i0_real_error	2.9570e+07
Rg (倒空间) rg_reciprocal	51.62 Å
I(0) (倒空间) i0_reciprocal	1737000000.0000
解质量估计 total_estimate	0.8483
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	69.8 Å
偏度 Skewness skewness	-0.004
峰度 Kurtosis kurtosis	-0.655
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	84420000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.996; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.058

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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 (2)

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6. 折叠分类 (SCOP + CATH) 48 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1ijga_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.27 — Upper collar protein gp10 (connector protein)
超家族 Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
家族 Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	d1ijgb_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.27 — Upper collar protein gp10 (connector protein)
超家族 Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
家族 Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	d1ijgc_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.27 — Upper collar protein gp10 (connector protein)
超家族 Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
家族 Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	d1ijgd_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.27 — Upper collar protein gp10 (connector protein)
超家族 Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
家族 Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	d1ijge_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.27 — Upper collar protein gp10 (connector protein)
超家族 Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
家族 Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	d1ijgf_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.27 — Upper collar protein gp10 (connector protein)
超家族 Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
家族 Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	d1ijgg_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.27 — Upper collar protein gp10 (connector protein)
超家族 Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
家族 Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	d1ijgh_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.27 — Upper collar protein gp10 (connector protein)
超家族 Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
家族 Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	d1ijgi_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.27 — Upper collar protein gp10 (connector protein)
超家族 Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
家族 Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	d1ijgj_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.27 — Upper collar protein gp10 (connector protein)
超家族 Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
家族 Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	d1ijgk_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.27 — Upper collar protein gp10 (connector protein)
超家族 Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
家族 Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	d1ijgl_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.27 — Upper collar protein gp10 (connector protein)
超家族 Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
家族 Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

CATH v4.4 (36 domains)

结构域编号 domain_id	1ijgA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1ijgA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	500 — Upper collar protein gp10 (connector protein) fold
同源超家族 H-superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	1ijgA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1350 — Crambin
同源超家族 H-superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

结构域编号 domain_id	1ijgB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1ijgB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	500 — Upper collar protein gp10 (connector protein) fold
同源超家族 H-superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	1ijgB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1350 — Crambin
同源超家族 H-superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

结构域编号 domain_id	1ijgC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1ijgC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	500 — Upper collar protein gp10 (connector protein) fold
同源超家族 H-superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	1ijgC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1350 — Crambin
同源超家族 H-superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

结构域编号 domain_id	1ijgD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1ijgD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	500 — Upper collar protein gp10 (connector protein) fold
同源超家族 H-superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	1ijgD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1350 — Crambin
同源超家族 H-superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

结构域编号 domain_id	1ijgE01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1ijgE02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	500 — Upper collar protein gp10 (connector protein) fold
同源超家族 H-superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	1ijgE03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1350 — Crambin
同源超家族 H-superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

结构域编号 domain_id	1ijgF01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1ijgF02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	500 — Upper collar protein gp10 (connector protein) fold
同源超家族 H-superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	1ijgF03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1350 — Crambin
同源超家族 H-superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

结构域编号 domain_id	1ijgG01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1ijgG02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	500 — Upper collar protein gp10 (connector protein) fold
同源超家族 H-superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	1ijgG03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1350 — Crambin
同源超家族 H-superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

结构域编号 domain_id	1ijgH01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1ijgH02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	500 — Upper collar protein gp10 (connector protein) fold
同源超家族 H-superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	1ijgH03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1350 — Crambin
同源超家族 H-superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

结构域编号 domain_id	1ijgI01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1ijgI02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	500 — Upper collar protein gp10 (connector protein) fold
同源超家族 H-superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	1ijgI03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1350 — Crambin
同源超家族 H-superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

结构域编号 domain_id	1ijgJ01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1ijgJ02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	500 — Upper collar protein gp10 (connector protein) fold
同源超家族 H-superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	1ijgJ03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1350 — Crambin
同源超家族 H-superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

结构域编号 domain_id	1ijgK01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1ijgK02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	500 — Upper collar protein gp10 (connector protein) fold
同源超家族 H-superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	1ijgK03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1350 — Crambin
同源超家族 H-superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

结构域编号 domain_id	1ijgL01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	246 — Serum Albumin; Chain A, Domain 1
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1ijgL02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	500 — Upper collar protein gp10 (connector protein) fold
同源超家族 H-superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

结构域编号 domain_id	1ijgL03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1350 — Crambin
同源超家族 H-superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

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7. 引用文献 (1)

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晶胞边长 a length_a	176.753 Å
晶胞边长 b length_b	171.568 Å
晶胞边长 c length_c	184.707 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	112.21 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	48

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	500.000 Å
R 因子 r_factor	0.2250
R_work r_work	0.2240
R_free r_free	0.2640

描述 description	UPPER COLLAR PROTEIN
分子量 formula_weight	35917.3 kDa
来源方法 src_method	man
拷贝数 entity_count	12

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L
原子数 atom_count	25977

Structure of the Bacteriophage phi29 Head-Tail Connector Protein

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 48 domains

SCOP 2.08 (12 domains)

CATH v4.4 (36 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

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	753

fit	/app/data/saxs_computation/ij/1ijg/1ijg.fit
pddf	/app/data/pr_computation/ij/1ijg/1ijg.pr.out
profile	/app/data/saxs_computation/ij/1ijg/1ijg.dat