1m3i

Perfringolysin O, new crystal form

Method: X-RAY DIFFRACTION D_max: 157.1 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1m3i
沉积日期 deposition_date	2002-06-28
结构标题 title	Perfringolysin O, new crystal form
关键词 keywords	pore forming toxin, TOXIN; TOXIN
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	48.69 Å
回转半径 Rg (电子) rg_electron	48.39 Å
零角强度 I(0) i0	625409000.00
分子量 molecular_weight	207280.0 kDa
排除体积 excluded_volume	259470 Å³
包络体积 envelope_volume	375020 Å³
水化壳体积 shell_volume	65220 Å³
包络直径 envelope_diameter	167.2 Å
壳层 Rg shell_rg	52.06 Å
包络 Rg envelope_rg	46.82 Å
形状 Rg shape_rg	48.38 Å
总 Rg total_rg	48.59 Å
总原子数 total_atoms	14628
残基数 n_residues	1860
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	157.1 Å
Rg (实空间) rg_real	48.54 Å
Rg 误差 (实空间) rg_real_error	1.36 Å
I(0) (实空间) i0_real	6.2540e+08
I(0) 误差 (实空间) i0_real_error	1.2080e+07
Rg (倒空间) rg_reciprocal	48.69 Å
I(0) (倒空间) i0_reciprocal	625500000.0000
解质量估计 total_estimate	0.8871
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	73.6 Å
偏度 Skewness skewness	0.111
峰度 Kurtosis kurtosis	-0.595
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	72930000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.851

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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 (2)

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1m3ia1
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.69 — Perfringolysin N-terminal-like
超家族 Superfamily superfamily	f.69.1 — Perfringolysin N-terminal-like
家族 Family family	f.69.1.1 — Perfringolysin N-terminal-like

结构域编号 domain_id	d1m3ia2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.183 — Perfringolysin C-terminal-like
超家族 Superfamily superfamily	b.183.1 — Perfringolysin C-terminal-like
家族 Family family	b.183.1.1 — Perfringolysin C-terminal-like

结构域编号 domain_id	d1m3ib1
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.69 — Perfringolysin N-terminal-like
超家族 Superfamily superfamily	f.69.1 — Perfringolysin N-terminal-like
家族 Family family	f.69.1.1 — Perfringolysin N-terminal-like

结构域编号 domain_id	d1m3ib2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.183 — Perfringolysin C-terminal-like
超家族 Superfamily superfamily	b.183.1 — Perfringolysin C-terminal-like
家族 Family family	b.183.1.1 — Perfringolysin C-terminal-like

结构域编号 domain_id	d1m3ic1
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.69 — Perfringolysin N-terminal-like
超家族 Superfamily superfamily	f.69.1 — Perfringolysin N-terminal-like
家族 Family family	f.69.1.1 — Perfringolysin N-terminal-like

结构域编号 domain_id	d1m3ic2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.183 — Perfringolysin C-terminal-like
超家族 Superfamily superfamily	b.183.1 — Perfringolysin C-terminal-like
家族 Family family	b.183.1.1 — Perfringolysin C-terminal-like

结构域编号 domain_id	d1m3id1
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.69 — Perfringolysin N-terminal-like
超家族 Superfamily superfamily	f.69.1 — Perfringolysin N-terminal-like
家族 Family family	f.69.1.1 — Perfringolysin N-terminal-like

结构域编号 domain_id	d1m3id2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.183 — Perfringolysin C-terminal-like
超家族 Superfamily superfamily	b.183.1 — Perfringolysin C-terminal-like
家族 Family family	b.183.1.1 — Perfringolysin C-terminal-like

CATH v4.4 (16 domains)

结构域编号 domain_id	1m3iA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	840 — HIV-1 Reverse Transcriptase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain

结构域编号 domain_id	1m3iA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1040 — Carboxypeptidase Inhibitor; Chain A
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1m3iA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	40 — Perfringolysin

结构域编号 domain_id	1m3iA04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1430 — Perfringolysin, domain 4

结构域编号 domain_id	1m3iB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	840 — HIV-1 Reverse Transcriptase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain

结构域编号 domain_id	1m3iB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1040 — Carboxypeptidase Inhibitor; Chain A
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1m3iB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	40 — Perfringolysin

结构域编号 domain_id	1m3iB04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1430 — Perfringolysin, domain 4

结构域编号 domain_id	1m3iC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	840 — HIV-1 Reverse Transcriptase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain

结构域编号 domain_id	1m3iC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1040 — Carboxypeptidase Inhibitor; Chain A
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1m3iC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	40 — Perfringolysin

结构域编号 domain_id	1m3iC04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1430 — Perfringolysin, domain 4

结构域编号 domain_id	1m3iD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	840 — HIV-1 Reverse Transcriptase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain

结构域编号 domain_id	1m3iD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1040 — Carboxypeptidase Inhibitor; Chain A
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1m3iD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	40 — Perfringolysin

结构域编号 domain_id	1m3iD04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1430 — Perfringolysin, domain 4

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7. 引用文献 (1)

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晶胞边长 a length_a	130.410 Å
晶胞边长 b length_b	130.410 Å
晶胞边长 c length_c	129.900 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	12

空间群 space_group	P 31
空间群编号 int_tables_number	144
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2330
R_free r_free	0.2800

描述 description	perfringolysin O
分子量 formula_weight	52571.5 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	14920

Perfringolysin O, new crystal form

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

CATH v4.4 (16 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Clostridium perfringens
NCBI 分类编号 ncbi_taxonomy_id	1502
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	292

fit	/app/data/saxs_computation/m3/1m3i/1m3i.fit
pddf	/app/data/pr_computation/m3/1m3i/1m3i.pr.out
profile	/app/data/saxs_computation/m3/1m3i/1m3i.dat