2iou

;Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella brochiseptica Virulence Factor Pertactin extracellular domain (Prn-E). ;

Method: X-RAY DIFFRACTION D_max: 196.9 Å Quality: REASONABLE

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	2iou
沉积日期 deposition_date	2006-10-10
结构标题 title	;Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella brochiseptica Virulence Factor Pertactin extracellular domain (Prn-E). ;
关键词 keywords	Mtd; Prn; pertactin, viral protein-membrane protein COMPLEX; viral protein/membrane 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	61.60 Å
回转半径 Rg (电子) rg_electron	62.24 Å
零角强度 I(0) i0	1712740000.00
分子量 molecular_weight	338370.0 kDa
排除体积 excluded_volume	419100 Å³
包络体积 envelope_volume	567080 Å³
水化壳体积 shell_volume	78754 Å³
包络直径 envelope_diameter	218.1 Å
壳层 Rg shell_rg	57.80 Å
包络 Rg envelope_rg	61.87 Å
形状 Rg shape_rg	62.21 Å
总 Rg total_rg	62.25 Å
总原子数 total_atoms	23900
残基数 n_residues	3272
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	196.9 Å
Rg (实空间) rg_real	62.17 Å
Rg 误差 (实空间) rg_real_error	1.72 Å
I(0) (实空间) i0_real	1.7120e+09
I(0) 误差 (实空间) i0_real_error	3.5490e+07
Rg (倒空间) rg_reciprocal	61.02 Å
I(0) (倒空间) i0_reciprocal	1709000000.0000
解质量估计 total_estimate	0.5580
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	47.3 Å
偏度 Skewness skewness	0.408
峰度 Kurtosis kurtosis	-0.709
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0015
最高正则化参数 α highest_alpha	138600000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.741; Stabil: 1.000; Sysdev: 0.004; Positv: 1.000; Valcen: 0.904; Smooth: 0.110

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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 (3)

Entity 1 polymer

描述 description	Major Tropism Determinant P1
分子量 formula_weight	39037.9 kDa
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,C,D,E,F
原子数 atom_count	23900

VQFRGGTTAQHATFTGAAREITVDTDKNTVVVHDGATAGGFPLARHDLVKTAFIKADKSAVAFTRTGNATASIKAGTIVEVNGKLVQFTADTAITMPALTAGTDYAIYVCDDGTVRADSNFSAPTGYTSTTARKVGGFHYAPGSNAAAQAGGNTTAQINEYSLWDIKFRPAALDPRGMTLVAGAFWADIYLLGVNHLTDGTSKYNVTIADGSASPKKSTKFGGDGSAAYSDGAWYNFAEVMTHHGKRLPNYNEFQALAFGTTEATSSGGTDVPTTGVNGTGATSAWNIFTSKWGVVQASGCLWTWGNEFGGVNGASEYTANTGGRGSVYAQPAAALFGGAWNGTSLSGSRAALWYSGPSFSFAFFGARGVCDHLIL

来源 Source

来源生物 organism	Bordetella phage BPP-1
NCBI 分类编号 ncbi_taxonomy_id	194699
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	Pertactin Extracellular Domain
分子量 formula_weight	54486.8 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

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

DWNNQSIIKAGERQHGIHIKQSDGAGVRTATGTTIKVSGRQAQGVLLENPAAELRFQNGSVTSSGQLFDEGVRRFLGTVTVKAGKLVADHATLANVSDTRDDDGIALYVAGEQAQASIADSTLQGAGGVRVERGANVTVQRSTIVDGGLHIGTLQPLQPEDLPPSRVVLGDTSVTAVPASGAPAAVSVFGANELTVDGGHITGGRAAGVAAMDGAIVHLQRATIRRGDAPAGGAVPGGAVPGGAVPGGFGPLLDGWYGVDVSDSTVDLAQSIVEAPQLGAAIRAGRGARVTVSGGSLSAPHGNVIETGGGARRFPPPASPLSITLQAGARAQGRALLYRVLPEPVKLTLAGGAQGQGDIVATELPPIPGASSGPLDVALASQARWTGATRAVDSLSIDNATWVMTDNSNVGALRLASDGSVDFQQPAEAGRFKVLMVDTLAGSGLFRMNVFADLGLSDKLVVMRDASGQHRLWVRNSGSEPASANTMLLVQTPRGSAATFTLANKDGKVDIGTYRYRLAANGNGQWSLVGAKAPP

来源 Source

来源生物 organism	Bordetella bronchiseptica
NCBI 分类编号 ncbi_taxonomy_id	257310
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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6. 折叠分类 (SCOP + CATH) 34 domains

SCOP 2.08 (14 domains)

结构域编号 domain_id	d2ioua1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.163 — Pseudo beta-prism I
超家族 Superfamily superfamily	b.163.1 — Bacteriophage trimeric proteins domain
家族 Family family	b.163.1.1 — Mtd domain-like

结构域编号 domain_id	d2ioua2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.8 — Mtd variable domain

结构域编号 domain_id	d2ioub1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.163 — Pseudo beta-prism I
超家族 Superfamily superfamily	b.163.1 — Bacteriophage trimeric proteins domain
家族 Family family	b.163.1.1 — Mtd domain-like

结构域编号 domain_id	d2ioub2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.8 — Mtd variable domain

结构域编号 domain_id	d2iouc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.163 — Pseudo beta-prism I
超家族 Superfamily superfamily	b.163.1 — Bacteriophage trimeric proteins domain
家族 Family family	b.163.1.1 — Mtd domain-like

结构域编号 domain_id	d2iouc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.8 — Mtd variable domain

结构域编号 domain_id	d2ioud1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.163 — Pseudo beta-prism I
超家族 Superfamily superfamily	b.163.1 — Bacteriophage trimeric proteins domain
家族 Family family	b.163.1.1 — Mtd domain-like

结构域编号 domain_id	d2ioud2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.8 — Mtd variable domain

结构域编号 domain_id	d2ioue1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.163 — Pseudo beta-prism I
超家族 Superfamily superfamily	b.163.1 — Bacteriophage trimeric proteins domain
家族 Family family	b.163.1.1 — Mtd domain-like

结构域编号 domain_id	d2ioue2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.8 — Mtd variable domain

结构域编号 domain_id	d2iouf1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.163 — Pseudo beta-prism I
超家族 Superfamily superfamily	b.163.1 — Bacteriophage trimeric proteins domain
家族 Family family	b.163.1.1 — Mtd domain-like

结构域编号 domain_id	d2iouf2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.8 — Mtd variable domain

结构域编号 domain_id	d2ioug_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.80 — Single-stranded right-handed beta-helix
超家族 Superfamily superfamily	b.80.1 — Pectin lyase-like
家族 Family family	b.80.1.7 — Virulence factor P.69 pertactin

结构域编号 domain_id	d2iouh_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.80 — Single-stranded right-handed beta-helix
超家族 Superfamily superfamily	b.80.1 — Pectin lyase-like
家族 Family family	b.80.1.7 — Virulence factor P.69 pertactin

CATH v4.4 (20 domains)

结构域编号 domain_id	2iouA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	2iouA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	20 — Tail fiber receptor-binding protein
同源超家族 H-superfamily homologous superfamily	10 — Tail fiber receptor-binding protein

结构域编号 domain_id	2iouA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1580 — paralog of FGE (formylglycine-generating enzyme)
同源超家族 H-superfamily homologous superfamily	10 — paralog of FGE (formylglycine-generating enzyme)

结构域编号 domain_id	2iouB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	2iouB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	20 — Tail fiber receptor-binding protein
同源超家族 H-superfamily homologous superfamily	10 — Tail fiber receptor-binding protein

结构域编号 domain_id	2iouB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1580 — paralog of FGE (formylglycine-generating enzyme)
同源超家族 H-superfamily homologous superfamily	10 — paralog of FGE (formylglycine-generating enzyme)

结构域编号 domain_id	2iouC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	2iouC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	20 — Tail fiber receptor-binding protein
同源超家族 H-superfamily homologous superfamily	10 — Tail fiber receptor-binding protein

结构域编号 domain_id	2iouC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1580 — paralog of FGE (formylglycine-generating enzyme)
同源超家族 H-superfamily homologous superfamily	10 — paralog of FGE (formylglycine-generating enzyme)

结构域编号 domain_id	2iouD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	2iouD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	20 — Tail fiber receptor-binding protein
同源超家族 H-superfamily homologous superfamily	10 — Tail fiber receptor-binding protein

结构域编号 domain_id	2iouD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1580 — paralog of FGE (formylglycine-generating enzyme)
同源超家族 H-superfamily homologous superfamily	10 — paralog of FGE (formylglycine-generating enzyme)

结构域编号 domain_id	2iouE01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	2iouE02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	20 — Tail fiber receptor-binding protein
同源超家族 H-superfamily homologous superfamily	10 — Tail fiber receptor-binding protein

结构域编号 domain_id	2iouE03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1580 — paralog of FGE (formylglycine-generating enzyme)
同源超家族 H-superfamily homologous superfamily	10 — paralog of FGE (formylglycine-generating enzyme)

结构域编号 domain_id	2iouF01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	2iouF02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	20 — Tail fiber receptor-binding protein
同源超家族 H-superfamily homologous superfamily	10 — Tail fiber receptor-binding protein

结构域编号 domain_id	2iouF03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1580 — paralog of FGE (formylglycine-generating enzyme)
同源超家族 H-superfamily homologous superfamily	10 — paralog of FGE (formylglycine-generating enzyme)

结构域编号 domain_id	2iouG00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	160 — 3 Solenoid
拓扑 Topology topology	20 — Pectate Lyase C-like
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2iouH00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	160 — 3 Solenoid
拓扑 Topology topology	20 — Pectate Lyase C-like
同源超家族 H-superfamily homologous superfamily	20 —

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7. 引用文献 (1)

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晶胞边长 a length_a	413.464 Å
晶胞边长 b length_b	413.464 Å
晶胞边长 c length_c	98.859 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 61
空间群编号 int_tables_number	169
晶系 crystal_system	—

分辨率 resolution	3.160 Å
最低分辨率 resolution_low	49.630 Å
R 因子 r_factor	0.2253
R_work r_work	0.2240
R_free r_free	0.2493

fit	/app/data/saxs_computation/io/2iou/2iou.fit
pddf	/app/data/pr_computation/io/2iou/2iou.pr.out
profile	/app/data/saxs_computation/io/2iou/2iou.dat

;Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella brochiseptica Virulence Factor Pertactin extracellular domain (Prn-E). ;

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

6. 折叠分类 (SCOP + CATH) 34 domains

SCOP 2.08 (14 domains)

CATH v4.4 (20 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)