SAXSdb — 1giq

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1giq
沉积日期 deposition_date	2001-03-12
结构标题 title	Crystal Structure of the Enzymatic Componet of Iota-Toxin from Clostridium Perfringens with NADH
关键词 keywords	enzymatic component, 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	40.31 Å
回转半径 Rg (电子) rg_electron	40.28 Å
零角强度 I(0) i0	136193000.00
分子量 molecular_weight	96024.0 kDa
排除体积 excluded_volume	120720 Å³
包络体积 envelope_volume	166080 Å³
水化壳体积 shell_volume	36131 Å³
包络直径 envelope_diameter	140.5 Å
壳层 Rg shell_rg	43.21 Å
包络 Rg envelope_rg	39.50 Å
形状 Rg shape_rg	40.27 Å
总 Rg total_rg	40.49 Å
总原子数 total_atoms	6782
残基数 n_residues	822
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	134.3 Å
Rg (实空间) rg_real	40.60 Å
Rg 误差 (实空间) rg_real_error	1.28 Å
I(0) (实空间) i0_real	1.3620e+08
I(0) 误差 (实空间) i0_real_error	2.3470e+06
Rg (倒空间) rg_reciprocal	40.31 Å
I(0) (倒空间) i0_reciprocal	136200000.0000
解质量估计 total_estimate	0.7941
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	31.0 Å
偏度 Skewness skewness	0.435
峰度 Kurtosis kurtosis	-0.579
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	14570000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.777; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.570; Smooth: 0.420

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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	IOTA TOXIN COMPONENT IA
分子量 formula_weight	47648.5 kDa
来源方法 src_method	nat
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	7068

AFIERPEDFLKDKENAIQWEKKEAERVEKNLDTLEKEALELYKKDSEQISNYSQTRQYFYDYQIESNPREKEYKNLRNAISKNKIDKPINVYYFESPEKFAFNKEIRTENQNEISLEKFNELKETIQDKLFKQDGFKDVSLYEPGNGDEKPTPLLIHLKLPKNTGMLPYINSNDVKTLIEQDYSIKIDKIVRIVIEGKQYIKAEASIVNSLDFKDDVSKGDLWGKENYSDWSNKLTPNELADVNDYMRGGYTAINNYLISNGPLNNPNPELDSKVNNIENALKLTPIPSNLIVYRRSGPQEFGLTLTSPEYDFNKIENIDAFKEKWEGKVITYPNFISTSIGSVNMSAFAKRKIILRINIPKDSPGAYLSAIPGYAGEYEVLLNHGSKFKINKVDSYKDGTVTKLILDATLIN

Entity 2 non-polymer

描述 description	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
分子量 formula_weight	665.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	286

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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	d1giqa1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.166 — ADP-ribosylation
超家族 Superfamily superfamily	d.166.1 — ADP-ribosylation
家族 Family family	d.166.1.1 — ADP-ribosylating toxins

结构域编号 domain_id	d1giqa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.166 — ADP-ribosylation
超家族 Superfamily superfamily	d.166.1 — ADP-ribosylation
家族 Family family	d.166.1.1 — ADP-ribosylating toxins

结构域编号 domain_id	d1giqb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.166 — ADP-ribosylation
超家族 Superfamily superfamily	d.166.1 — ADP-ribosylation
家族 Family family	d.166.1.1 — ADP-ribosylating toxins

结构域编号 domain_id	d1giqb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.166 — ADP-ribosylation
超家族 Superfamily superfamily	d.166.1 — ADP-ribosylation
家族 Family family	d.166.1.1 — ADP-ribosylating toxins

CATH v4.4 (4 domains)

结构域编号 domain_id	1giqA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

结构域编号 domain_id	1giqA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

结构域编号 domain_id	1giqB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

结构域编号 domain_id	1giqB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

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7. 引用文献 (1)

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晶胞边长 a length_a	48.200 Å
晶胞边长 b length_b	54.440 Å
晶胞边长 c length_c	103.380 Å
晶胞夹角 α angle_alpha	99.20 °
晶胞夹角 β angle_beta	93.10 °
晶胞夹角 γ angle_gamma	106.90 °
晶胞分子数 Z z_pdb	2

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

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	14.970 Å
R 因子 r_factor	—
R_work r_work	0.2240
R_free r_free	0.2500

fit	/app/data/saxs_computation/gi/1giq/1giq.fit
pddf	/app/data/pr_computation/gi/1giq/1giq.pr.out
profile	/app/data/saxs_computation/gi/1giq/1giq.dat

Crystal Structure of the Enzymatic Componet of Iota-Toxin from Clostridium Perfringens with NADH

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