2hqs

Crystal structure of TolB/Pal complex

Method: X-RAY DIFFRACTION D_max: 136.0 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	2hqs
沉积日期 deposition_date	2006-07-19
结构标题 title	Crystal structure of TolB/Pal complex
关键词 keywords	TolB, Pal, Tol, TRANSPORT PROTEIN-LIPOPROTEIN COMPLEX; TRANSPORT PROTEIN/LIPOPROTEIN
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	42.79 Å
回转半径 Rg (电子) rg_electron	42.30 Å
零角强度 I(0) i0	788439000.00
分子量 molecular_weight	225120.0 kDa
排除体积 excluded_volume	279110 Å³
包络体积 envelope_volume	373790 Å³
水化壳体积 shell_volume	72188 Å³
包络直径 envelope_diameter	144.3 Å
壳层 Rg shell_rg	49.02 Å
包络 Rg envelope_rg	41.34 Å
形状 Rg shape_rg	42.31 Å
总 Rg total_rg	42.61 Å
总原子数 total_atoms	15890
残基数 n_residues	2072
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	136.0 Å
Rg (实空间) rg_real	42.61 Å
Rg 误差 (实空间) rg_real_error	0.88 Å
I(0) (实空间) i0_real	7.8840e+08
I(0) 误差 (实空间) i0_real_error	1.3110e+07
Rg (倒空间) rg_reciprocal	42.79 Å
I(0) (倒空间) i0_reciprocal	788600000.0000
解质量估计 total_estimate	0.8853
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	55.1 Å
偏度 Skewness skewness	0.166
峰度 Kurtosis kurtosis	-0.371
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	68310000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.866

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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 (6)

Entity 1 polymer

描述 description	Protein tolB
分子量 formula_weight	44468.3 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,D,F
原子数 atom_count	18839

MVRIVIDSGVDSGRPIGVVPFQWAGPGAAPEDIGGIVAADLRNSGKFNPLDRARLPQQPGSAQEVQPAAWSALGIDAVVVGQVTPNPDGSYNVAYQLVDTGGAPGTVLAQNSYKVNKQWLRYAGHTASDEVFEKLTGIKGAFRTRIAYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYVTFESGRSALVIQTLANGAVRQVASFPRHNGAPAFSPDGSKLAFALSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTWFPDSQNLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQDADVSSDGKFMVMVSSNGGQQHIAKQDLATGGVQVLSSTFLDETPSLAPNGTMVIYSSSQGMGSVLNLVSTDGRFKARLPATDGQVKFPAWSPYLHHHHHH

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 polymer

描述 description	Peptidoglycan-associated lipoprotein
分子量 formula_weight	13518.1 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H,C,E,G

MLQQNNIVYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNISLGERRANAVKMYLQGKGVSADQISIVSYGKEKPAVLGHDEAAYSKNRRAVLVYLEHHHHHH

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 3 non-polymer

描述 description	ACETATE ION
分子量 formula_weight	59.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 4 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 5 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 6 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	2812

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6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (20 domains)

结构域编号 domain_id	d2hqsa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.4 — TolB, C-terminal domain
家族 Family family	b.68.4.1 — TolB, C-terminal domain

结构域编号 domain_id	d2hqsa2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.2 — TolB, N-terminal domain
家族 Family family	c.51.2.1 — TolB, N-terminal domain

结构域编号 domain_id	d2hqsa3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2hqsb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.4 — TolB, C-terminal domain
家族 Family family	b.68.4.1 — TolB, C-terminal domain

结构域编号 domain_id	d2hqsb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.2 — TolB, N-terminal domain
家族 Family family	c.51.2.1 — TolB, N-terminal domain

结构域编号 domain_id	d2hqsb3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2hqsc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.7 — OmpA-like
家族 Family family	d.79.7.1 — OmpA-like

结构域编号 domain_id	d2hqsc3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2hqsd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.4 — TolB, C-terminal domain
家族 Family family	b.68.4.1 — TolB, C-terminal domain

结构域编号 domain_id	d2hqsd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.2 — TolB, N-terminal domain
家族 Family family	c.51.2.1 — TolB, N-terminal domain

结构域编号 domain_id	d2hqsd3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2hqse2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.7 — OmpA-like
家族 Family family	d.79.7.1 — OmpA-like

结构域编号 domain_id	d2hqse3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2hqsf1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.4 — TolB, C-terminal domain
家族 Family family	b.68.4.1 — TolB, C-terminal domain

结构域编号 domain_id	d2hqsf2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.2 — TolB, N-terminal domain
家族 Family family	c.51.2.1 — TolB, N-terminal domain

结构域编号 domain_id	d2hqsf3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2hqsg2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.7 — OmpA-like
家族 Family family	d.79.7.1 — OmpA-like

结构域编号 domain_id	d2hqsg3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2hqsh2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.7 — OmpA-like
家族 Family family	d.79.7.1 — OmpA-like

结构域编号 domain_id	d2hqsh3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (12 domains)

结构域编号 domain_id	2hqsA01
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	10070 — TolB, N-terminal domain

结构域编号 domain_id	2hqsA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	30 — TolB, C-terminal domain

结构域编号 domain_id	2hqsB01
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	10070 — TolB, N-terminal domain

结构域编号 domain_id	2hqsB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	30 — TolB, C-terminal domain

结构域编号 domain_id	2hqsC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	60 — OmpA-like domain

结构域编号 domain_id	2hqsD01
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	10070 — TolB, N-terminal domain

结构域编号 domain_id	2hqsD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	30 — TolB, C-terminal domain

结构域编号 domain_id	2hqsE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	60 — OmpA-like domain

结构域编号 domain_id	2hqsF01
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	10070 — TolB, N-terminal domain

结构域编号 domain_id	2hqsF02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	30 — TolB, C-terminal domain

结构域编号 domain_id	2hqsG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	60 — OmpA-like domain

结构域编号 domain_id	2hqsH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	60 — OmpA-like domain

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7. 引用文献 (1)

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晶胞边长 a length_a	74.847 Å
晶胞边长 b length_b	89.049 Å
晶胞边长 c length_c	91.051 Å
晶胞夹角 α angle_alpha	87.15 °
晶胞夹角 β angle_beta	89.62 °
晶胞夹角 γ angle_gamma	68.81 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	1.500 Å
最低分辨率 resolution_low	38.320 Å
R 因子 r_factor	0.1820
R_work r_work	0.1804
R_free r_free	0.2127

fit	/app/data/saxs_computation/hq/2hqs/2hqs.fit
pddf	/app/data/pr_computation/hq/2hqs/2hqs.pr.out
profile	/app/data/saxs_computation/hq/2hqs/2hqs.dat

Crystal structure of TolB/Pal complex

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 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (20 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)