1gl7

Plasmid coupling protein TrwB in complex with the non-hydrolisable ATP-analogue ADPNP.

Method: X-RAY DIFFRACTION D_max: 113.1 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	1gl7
沉积日期 deposition_date	2001-08-28
结构标题 title	Plasmid coupling protein TrwB in complex with the non-hydrolisable ATP-analogue ADPNP.
关键词 keywords	COUPLING PROTEIN, TYPE IV SECRETION SYSTEM CONJUGATIVE COUPLING PROTEIN FROM PLASMID; COUPLING 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	39.58 Å
回转半径 Rg (电子) rg_electron	38.52 Å
零角强度 I(0) i0	1171720000.00
分子量 molecular_weight	279910.0 kDa
排除体积 excluded_volume	349960 Å³
包络体积 envelope_volume	443580 Å³
水化壳体积 shell_volume	88605 Å³
包络直径 envelope_diameter	115.2 Å
壳层 Rg shell_rg	49.72 Å
包络 Rg envelope_rg	37.70 Å
形状 Rg shape_rg	38.53 Å
总 Rg total_rg	39.04 Å
总原子数 total_atoms	19700
残基数 n_residues	2484
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	113.1 Å
Rg (实空间) rg_real	39.13 Å
Rg 误差 (实空间) rg_real_error	0.43 Å
I(0) (实空间) i0_real	1.1720e+09
I(0) 误差 (实空间) i0_real_error	1.6410e+07
Rg (倒空间) rg_reciprocal	39.41 Å
I(0) (倒空间) i0_reciprocal	1172000000.0000
解质量估计 total_estimate	0.8311
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	53.7 Å
偏度 Skewness skewness	-0.044
峰度 Kurtosis kurtosis	-0.605
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	671600000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.000

▶

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

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	CONJUGAL TRANSFER PROTEIN TRWB
分子量 formula_weight	48671.5 kDa
突变 mutation	YES
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,D,E,F,G
原子数 atom_count	19892

LNSVGQGEFGGAPFKRFLRGTRIVSGGKLKRMTREKAKQVTVAGVPMPRDAEPRHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPNGDMLSKFGRDKDIILNPYDQRTKGWSFFNEIRNDYDWQRYALSVVPRGKTDEAEEWASYGRLLLRETAKKLALIGTPSMRELFHWTTIATFDDLRGFLEGTLAESLFAGSNEASKALTSARFVLSDKLPEHVTMPDGDFSIRSWLEDPNGGNLFITWREDMGPALRPLISAWVDVVCTSILSLPEEPKRRLWLFIDELASLEKLASLADALTKGRKAGLRVVAGLQSTSQLDDVYGVKEAQTLRASFRSLVVLGGSRTDPKTNEDMSLSLGEHEVERDRYSKNTGKHHSTGRALERVRERVVMPAEIANLPDLTAYVGFAGNRPIAKVPLEIKQFANRQPAFVEGTI

来源 Source

来源生物 organism	ESCHERICHIA COLI
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
分子量 formula_weight	506.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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	1

Entity 4 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	192

▼

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1gl7a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

结构域编号 domain_id	d1gl7b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

结构域编号 domain_id	d1gl7d_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

结构域编号 domain_id	d1gl7e_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

结构域编号 domain_id	d1gl7f_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

结构域编号 domain_id	d1gl7g_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

CATH v4.4 (12 domains)

结构域编号 domain_id	1gl7A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1gl7A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	80 — Magnesium chelatase subunit I, C-Terminal domain

结构域编号 domain_id	1gl7B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1gl7B02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	80 — Magnesium chelatase subunit I, C-Terminal domain

结构域编号 domain_id	1gl7D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1gl7D02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	80 — Magnesium chelatase subunit I, C-Terminal domain

结构域编号 domain_id	1gl7E01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1gl7E02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	80 — Magnesium chelatase subunit I, C-Terminal domain

结构域编号 domain_id	1gl7F01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1gl7F02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	80 — Magnesium chelatase subunit I, C-Terminal domain

结构域编号 domain_id	1gl7G01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1gl7G02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	80 — Magnesium chelatase subunit I, C-Terminal domain

▶

7. 引用文献 (2)

▶

晶胞边长 a length_a	152.700 Å
晶胞边长 b length_b	152.700 Å
晶胞边长 c length_c	252.100 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	120.00 °
晶胞分子数 Z z_pdb	36

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2650

fit	/app/data/saxs_computation/gl/1gl7/1gl7.fit
pddf	/app/data/pr_computation/gl/1gl7/1gl7.pr.out
profile	/app/data/saxs_computation/gl/1gl7/1gl7.dat