1jnb

CONNECTOR PROTEIN FROM BACTERIOPHAGE PHI29

Method: X-RAY DIFFRACTION D_max: 145.9 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	1jnb
沉积日期 deposition_date	2001-07-23
结构标题 title	CONNECTOR PROTEIN FROM BACTERIOPHAGE PHI29
关键词 keywords	helix bundle, 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	51.21 Å
回转半径 Rg (电子) rg_electron	50.59 Å
零角强度 I(0) i0	1737880000.00
分子量 molecular_weight	357060.0 kDa
排除体积 excluded_volume	449460 Å³
包络体积 envelope_volume	636870 Å³
水化壳体积 shell_volume	101230 Å³
包络直径 envelope_diameter	150.9 Å
壳层 Rg shell_rg	58.74 Å
包络 Rg envelope_rg	48.67 Å
形状 Rg shape_rg	50.58 Å
总 Rg total_rg	50.88 Å
总原子数 total_atoms	25236
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	145.9 Å
Rg (实空间) rg_real	50.96 Å
Rg 误差 (实空间) rg_real_error	1.00 Å
I(0) (实空间) i0_real	1.7380e+09
I(0) 误差 (实空间) i0_real_error	3.0820e+07
Rg (倒空间) rg_reciprocal	51.41 Å
I(0) (倒空间) i0_reciprocal	1739000000.0000
解质量估计 total_estimate	0.8523
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	65.9 Å
偏度 Skewness skewness	-0.002
峰度 Kurtosis kurtosis	-0.650
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	78260000.0000
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: 0.991; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.127

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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) 48 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1jnba_
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	d1jnbb_
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	d1jnbc_
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	d1jnbd_
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	d1jnbe_
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	d1jnbf_
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	d1jnbg_
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	d1jnbh_
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	d1jnbi_
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	d1jnbj_
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	d1jnbk_
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	d1jnbl_
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	1jnbA01
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	1jnbA02
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	1jnbA03
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	1jnbB01
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	1jnbB02
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	1jnbB03
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	1jnbC01
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	1jnbC02
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	1jnbC03
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	1jnbD01
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	1jnbD02
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	1jnbD03
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	1jnbE01
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	1jnbE02
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	1jnbE03
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	1jnbF01
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	1jnbF02
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	1jnbF03
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	1jnbG01
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	1jnbG02
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	1jnbG03
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	1jnbH01
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	1jnbH02
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	1jnbH03
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	1jnbI01
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	1jnbI02
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	1jnbI03
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	1jnbJ01
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	1jnbJ02
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	1jnbJ03
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	1jnbK01
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	1jnbK02
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	1jnbK03
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	1jnbL01
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	1jnbL02
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	1jnbL03
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 (2)

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晶胞边长 a length_a	177.160 Å
晶胞边长 b length_b	169.240 Å
晶胞边长 c length_c	185.440 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	114.10 °
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	3.200 Å
最低分辨率 resolution_low	9.000 Å
R 因子 r_factor	0.2866
R_work r_work	0.2844
R_free r_free	0.3014

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	25236

CONNECTOR PROTEIN FROM BACTERIOPHAGE PHI29

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) 48 domains

SCOP 2.08 (12 domains)

CATH v4.4 (36 domains)

7. 引用文献 (2)

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/jn/1jnb/1jnb.fit
pddf	/app/data/pr_computation/jn/1jnb/1jnb.pr.out
profile	/app/data/saxs_computation/jn/1jnb/1jnb.dat