SAXSdb — 1gzf

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1gzf
沉积日期 deposition_date	2002-05-21
结构标题 title	Structure of the Clostridium botulinum C3 exoenzyme (wild-type) in complex with NAD
关键词 keywords	TRANSFERASE, ADP-RIBOSYLTRANSFERASE, BACTERIAL TOXIN, C3 EXOENZYME; TRANSFERASE
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	30.15 Å
回转半径 Rg (电子) rg_electron	29.46 Å
零角强度 I(0) i0	145140000.00
分子量 molecular_weight	94810.0 kDa
排除体积 excluded_volume	118610 Å³
包络体积 envelope_volume	146670 Å³
水化壳体积 shell_volume	41093 Å³
包络直径 envelope_diameter	96.8 Å
壳层 Rg shell_rg	36.93 Å
包络 Rg envelope_rg	29.06 Å
形状 Rg shape_rg	29.44 Å
总 Rg total_rg	30.19 Å
总原子数 total_atoms	6653
残基数 n_residues	825
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	92.1 Å
Rg (实空间) rg_real	29.98 Å
Rg 误差 (实空间) rg_real_error	0.42 Å
I(0) (实空间) i0_real	1.4510e+08
I(0) 误差 (实空间) i0_real_error	2.0530e+06
Rg (倒空间) rg_reciprocal	30.06 Å
I(0) (倒空间) i0_reciprocal	145100000.0000
解质量估计 total_estimate	0.9061
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	40.0 Å
偏度 Skewness skewness	0.127
峰度 Kurtosis kurtosis	-0.515
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	63280000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.944

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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	MONO-ADP-RIBOSYLTRANSFERASE C3
分子量 formula_weight	23592.0 kDa
EC 编号 ec_number	2.4.2.-
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,C,D
原子数 atom_count	7223

AYSNTYQEFTNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKGVINGFPSNLIKQVELLDKSFNKMKTPENIMLFRGDDPAYLGTEFQNTLLNSNGTINKTAFEKAKAKFLNKDRLEYGYISTSLMNVSQFAGRPIITKFKVAKGSKAGYIDPISAFAGQLEMLLPRHSTYHIDDMRLSSDGKQIIITATMMGTAINPK

来源 Source

来源生物 organism	CLOSTRIDIUM BOTULINUM
NCBI 分类编号 ncbi_taxonomy_id	1491
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 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	2

Entity 4 non-polymer

描述 description	3-(AMINOCARBONYL)-1-[(3R,4S,5R)-3,4-DIHYDROXY-5-METHYLTETRAHYDRO-2-FURANYL]PYRIDINIUM
分子量 formula_weight	242.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	570

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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	d1gzfa_
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	d1gzfb_
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	d1gzfc_
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	d1gzfd_
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	1gzfA00
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	1gzfB00
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	1gzfC00
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	1gzfD00
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	103.947 Å
晶胞边长 b length_b	74.191 Å
晶胞边长 c length_c	119.680 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	102.10 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.950 Å
最低分辨率 resolution_low	25.000 Å
R 因子 r_factor	0.2340
R_work r_work	0.2340
R_free r_free	0.2770

fit	/app/data/saxs_computation/gz/1gzf/1gzf.fit
pddf	/app/data/pr_computation/gz/1gzf/1gzf.pr.out
profile	/app/data/saxs_computation/gz/1gzf/1gzf.dat

Structure of the Clostridium botulinum C3 exoenzyme (wild-type) in complex with NAD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution