SAXSdb — 1kho

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1kho
沉积日期 deposition_date	2001-11-30
结构标题 title	Crystal Structure Analysis of Clostridium perfringens alpha-Toxin Isolated from Avian Strain SWCP
关键词 keywords	N-terminal alpha-helix, C-terminal beta-sheet, 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	29.34 Å
回转半径 Rg (电子) rg_electron	28.58 Å
零角强度 I(0) i0	125172000.00
分子量 molecular_weight	85109.0 kDa
排除体积 excluded_volume	104820 Å³
包络体积 envelope_volume	128900 Å³
水化壳体积 shell_volume	37336 Å³
包络直径 envelope_diameter	102.7 Å
壳层 Rg shell_rg	36.27 Å
包络 Rg envelope_rg	28.31 Å
形状 Rg shape_rg	28.55 Å
总 Rg total_rg	29.36 Å
总原子数 total_atoms	5996
残基数 n_residues	740
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	93.8 Å
Rg (实空间) rg_real	29.27 Å
Rg 误差 (实空间) rg_real_error	0.56 Å
I(0) (实空间) i0_real	1.2520e+08
I(0) 误差 (实空间) i0_real_error	1.7500e+06
Rg (倒空间) rg_reciprocal	29.30 Å
I(0) (倒空间) i0_reciprocal	125200000.0000
解质量估计 total_estimate	0.7229
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	34.7 Å
偏度 Skewness skewness	0.246
峰度 Kurtosis kurtosis	-0.477
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	31340000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 0.218; Positv: 1.000; Valcen: 1.000; Smooth: 0.965

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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	alpha-toxin
分子量 formula_weight	42421.3 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	A,B
原子数 atom_count	6148

WDGKADGTGTHAMIATQGVTILENDLSSNEPEVIRNNLEILKQNMHDLQLGSTYPDYDKNAYDLYQDHFWDPDTDNNFTKDSKWYLSYSIPDTAESQIRKFSALARYEWKRGNYKQATFYLGEAMHYFGDADTPYHAANVTAVDSPGHVKFETFAEDRKDQYKINTTGSKTNDAFYSNILTNEDFNSWSKEFARSFAKTAKDLYYSHANMSCSWDEWDYAAKVALANSQKGTSGYIYRFLHDVSDGKDSSANKNVNELVAYITTGGEKYAGTDDYMYFGIKTKDGQTQEWTMDNPGNDFMTGSQDTYTFKLKDKNLKIDDIQNMWIRKSKYTEFGDDYKPANIKVIANGNVVLNKDINEWISGNSTYNIK

来源 Source

来源生物 organism	Clostridium perfringens
NCBI 分类编号 ncbi_taxonomy_id	1502
宿主生物 host_organism	Escherichia coli BL21

Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 3 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	152

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1khoa1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.124 — Phospholipase C/P1 nuclease
超家族 Superfamily superfamily	a.124.1 — Phospholipase C/P1 nuclease
家族 Family family	a.124.1.1 — Phospholipase C

结构域编号 domain_id	d1khoa2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.12 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
超家族 Superfamily superfamily	b.12.1 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
家族 Family family	b.12.1.3 — Alpha-toxin, C-terminal domain

结构域编号 domain_id	d1khob1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.124 — Phospholipase C/P1 nuclease
超家族 Superfamily superfamily	a.124.1 — Phospholipase C/P1 nuclease
家族 Family family	a.124.1.1 — Phospholipase C

结构域编号 domain_id	d1khob2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.12 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
超家族 Superfamily superfamily	b.12.1 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
家族 Family family	b.12.1.3 — Alpha-toxin, C-terminal domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1khoA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	575 — P1 Nuclease
同源超家族 H-superfamily homologous superfamily	10 — P1 Nuclease

结构域编号 domain_id	1khoA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	60 — Lipoxygenase-1
同源超家族 H-superfamily homologous superfamily	20 — PLAT/LH2 domain

结构域编号 domain_id	1khoB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	575 — P1 Nuclease
同源超家族 H-superfamily homologous superfamily	10 — P1 Nuclease

结构域编号 domain_id	1khoB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	60 — Lipoxygenase-1
同源超家族 H-superfamily homologous superfamily	20 — PLAT/LH2 domain

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7. 引用文献 (1)

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晶胞边长 a length_a	117.230 Å
晶胞边长 b length_b	117.230 Å
晶胞边长 c length_c	220.590 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	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	P 41 2 2
空间群编号 int_tables_number	91
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.2098
R_free r_free	0.2361

fit	/app/data/saxs_computation/kh/1kho/1kho.fit
pddf	/app/data/pr_computation/kh/1kho/1kho.pr.out
profile	/app/data/saxs_computation/kh/1kho/1kho.dat

Crystal Structure Analysis of Clostridium perfringens alpha-Toxin Isolated from Avian Strain SWCP

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