SAXSdb — 2c8g

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2c8g
沉积日期 deposition_date	2005-12-03
结构标题 title	Structure of the PN loop Q182A mutant C3bot1 Exoenzyme (Free state, crystal form I)
关键词 keywords	C3 EXOENZYME, ARTT MOTIF, ADP-RIBOSYLTRANSFERASE, BACTERIAL TOXINS, TRANSFERASE, GLYCOSYLTRANSFERASE; 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	30.65 Å
回转半径 Rg (电子) rg_electron	29.88 Å
零角强度 I(0) i0	131599000.00
分子量 molecular_weight	91681.0 kDa
排除体积 excluded_volume	115440 Å³
包络体积 envelope_volume	149670 Å³
水化壳体积 shell_volume	41479 Å³
包络直径 envelope_diameter	97.5 Å
壳层 Rg shell_rg	37.29 Å
包络 Rg envelope_rg	29.39 Å
形状 Rg shape_rg	29.86 Å
总 Rg total_rg	30.64 Å
总原子数 total_atoms	6443
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	93.6 Å
Rg (实空间) rg_real	30.47 Å
Rg 误差 (实空间) rg_real_error	0.47 Å
I(0) (实空间) i0_real	1.3160e+08
I(0) 误差 (实空间) i0_real_error	1.5990e+06
Rg (倒空间) rg_reciprocal	30.55 Å
I(0) (倒空间) i0_reciprocal	131600000.0000
解质量估计 total_estimate	0.9068
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	41.4 Å
偏度 Skewness skewness	0.118
峰度 Kurtosis kurtosis	-0.525
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	40680000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.949

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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	MONO-ADP-RIBOSYLTRANSFERASE C3
分子量 formula_weight	23534.9 kDa
EC 编号 ec_number	2.4.2.-
突变 mutation	YES
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	6747

AYSNTYQEFTNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKGVINGFPSNLIKQVELLDKSFNKMKTPENIMLFRGDDPAYLGTEFQNTLLNSNGTINKTAFEKAKAKFLNKDRLEYGYISTSLMNVSAFAGRPIITKFKVAKGSKAGYIDPISAFAGQLEMLLPRHSTYHIDDMRLSSDGKQIIITATMMGTAINPK

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	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	298

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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	d2c8ga_
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	d2c8gb_
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	d2c8gc_
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	d2c8gd_
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	2c8gA00
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	2c8gB00
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	2c8gC00
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	2c8gD00
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 (2)

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晶胞边长 a length_a	105.671 Å
晶胞边长 b length_b	74.951 Å
晶胞边长 c length_c	121.199 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	102.46 °
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	2.000 Å
最低分辨率 resolution_low	39.840 Å
R 因子 r_factor	0.2130
R_work r_work	0.2120
R_free r_free	0.2470

fit	/app/data/saxs_computation/c8/2c8g/2c8g.fit
pddf	/app/data/pr_computation/c8/2c8g/2c8g.pr.out
profile	/app/data/saxs_computation/c8/2c8g/2c8g.dat

Structure of the PN loop Q182A mutant C3bot1 Exoenzyme (Free state, crystal form I)

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