1gl6

Plasmid coupling protein TrwB in complex with the non-hydrolysable GTP analogue GDPNP

Method: X-RAY DIFFRACTION D_max: 111.6 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	1gl6
沉积日期 deposition_date	2001-08-28
结构标题 title	Plasmid coupling protein TrwB in complex with the non-hydrolysable GTP analogue GDPNP
关键词 keywords	COUPLING PROTEIN, TYPE IV SECRETION SYSTEM, BACTERIAL CONJUG PROTEIN, RING HELICASE; COUPLING 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	39.37 Å
回转半径 Rg (电子) rg_electron	38.30 Å
零角强度 I(0) i0	1198560000.00
分子量 molecular_weight	282180.0 kDa
排除体积 excluded_volume	352410 Å³
包络体积 envelope_volume	441210 Å³
水化壳体积 shell_volume	88528 Å³
包络直径 envelope_diameter	114.5 Å
壳层 Rg shell_rg	49.57 Å
包络 Rg envelope_rg	37.50 Å
形状 Rg shape_rg	38.30 Å
总 Rg total_rg	38.82 Å
总原子数 total_atoms	19852
残基数 n_residues	2498
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	111.6 Å
Rg (实空间) rg_real	38.92 Å
Rg 误差 (实空间) rg_real_error	0.36 Å
I(0) (实空间) i0_real	1.1990e+09
I(0) 误差 (实空间) i0_real_error	1.6660e+07
Rg (倒空间) rg_reciprocal	39.20 Å
I(0) (倒空间) i0_reciprocal	1199000000.0000
解质量估计 total_estimate	0.8941
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	55.8 Å
偏度 Skewness skewness	-0.050
峰度 Kurtosis kurtosis	-0.609
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	707600000.0000
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: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.803

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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 (5)

Entity 1 polymer

描述 description	ATPASE
分子量 formula_weight	48558.3 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	20441

NSVGQGEFGGAPFKRFLRGTRIVSGGKLKRMTREKAKQVTVAGVPMPRDAEPRHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPNGDMLSKFGRDKDIILNPYDQRTKGWSFFNEIRNDYDWQRYALSVVPRGKTDEAEEWASYGRLLLRETAKKLALIGTPSMRELFHWTTIATFDDLRGFLEGTLAESLFAGSNEASKALTSARFVLSDKLPEHVTMPDGDFSIRSWLEDPNGGNLFITWREDMGPALRPLISAWVDVVCTSILSLPEEPKRRLWLFIDELASLEKLASLADALTKGRKAGLRVVAGLQSTSQLDDVYGVKEAQTLRASFRSLVVLGGSRTDPKTNEDMSLSLGEHEVERDRYSKNTGKHHSTGRALERVRERVVMPAEIANLPDLTAYVGFAGNRPIAKVPLEIKQFANRQPAFVEGTI

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-GUANYLATE ESTER
分子量 formula_weight	522.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

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 non-polymer

描述 description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
分子量 formula_weight	238.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	589

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1gl6a_
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	d1gl6b_
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	d1gl6d_
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	d1gl6e_
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	d1gl6f_
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	d1gl6g_
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	1gl6A01
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	1gl6A02
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	1gl6B01
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	1gl6B02
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	1gl6D01
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	1gl6D02
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	1gl6E01
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	1gl6E02
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	1gl6F01
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	1gl6F02
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	1gl6G01
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	1gl6G02
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

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7. 引用文献 (2)

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晶胞边长 a length_a	151.600 Å
晶胞边长 b length_b	151.600 Å
晶胞边长 c length_c	252.000 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	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	2.800 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2140
R_work r_work	0.2140
R_free r_free	0.2580

fit	/app/data/saxs_computation/gl/1gl6/1gl6.fit
pddf	/app/data/pr_computation/gl/1gl6/1gl6.pr.out
profile	/app/data/saxs_computation/gl/1gl6/1gl6.dat