SAXSdb — 2adm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2adm
沉积日期 deposition_date	1996-07-15
结构标题 title	ADENINE-N6-DNA-METHYLTRANSFERASE TAQI
关键词 keywords	TRANSFERASE, METHYLTRANSFERASE, RESTRICTION SYSTEM; METHYLTRANSFERASE
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	32.99 Å
回转半径 Rg (电子) rg_electron	32.22 Å
零角强度 I(0) i0	111832000.00
分子量 molecular_weight	88773.0 kDa
排除体积 excluded_volume	113040 Å³
包络体积 envelope_volume	143910 Å³
水化壳体积 shell_volume	38036 Å³
包络直径 envelope_diameter	109.9 Å
壳层 Rg shell_rg	38.33 Å
包络 Rg envelope_rg	31.67 Å
形状 Rg shape_rg	32.21 Å
总 Rg total_rg	32.80 Å
总原子数 total_atoms	6300
残基数 n_residues	770
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	108.0 Å
Rg (实空间) rg_real	32.95 Å
Rg 误差 (实空间) rg_real_error	0.86 Å
I(0) (实空间) i0_real	1.1180e+08
I(0) 误差 (实空间) i0_real_error	1.9830e+06
Rg (倒空间) rg_reciprocal	32.97 Å
I(0) (倒空间) i0_reciprocal	111800000.0000
解质量估计 total_estimate	0.8963
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	40.5 Å
偏度 Skewness skewness	0.249
峰度 Kurtosis kurtosis	-0.472
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	17270000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.903

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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	ADENINE-N6-DNA-METHYLTRANSFERASE TAQI
分子量 formula_weight	47931.2 kDa
EC 编号 ec_number	2.1.1.72
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	6394

MGLPPLLSLPSNSAPRSLGRVETPPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREAHGTGYRFVGVEIDPKALDLPPWAEGILADFLLWEPGEAFDLILGNPPYGIVGEASKYPIHVFKAVKDLYKKAFSTWKGKYNLYGAFLEKAVRLLKPGGVLVFVVPATWLVLEDFALLREFLAREGKTSVYYLGEVFPQKKVSAVVIRFQKSGKGLSLWDTQESESGFTPILWAEYPHWEGEIIRFETEETRKLEISGMPLGDLFHIRFAARSPEFKKHPAVRKEPGPGLVPVLTGRNLKPGWVDYEKNHSGLWMPKERAKELRDFYATPHLVVAHTKGTRVVAAWDERAYPWREEFHLLPKEGVRLDPSTLVQWLNSEAMQKHVRTLYRDFVPHLTLRMLERLPVRREYGFHTSPESARNF

来源 Source

来源生物 organism	Thermus aquaticus
NCBI 分类编号 ncbi_taxonomy_id	271
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	S-ADENOSYLMETHIONINE
分子量 formula_weight	398.4 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	94

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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	d2adma1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.27 — DNA methylase TaqI, N-terminal domain

结构域编号 domain_id	d2adma2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.287 — DNA methylase specificity domain
超家族 Superfamily superfamily	d.287.1 — DNA methylase specificity domain
家族 Family family	d.287.1.1 — TaqI C-terminal domain-like

结构域编号 domain_id	d2admb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.27 — DNA methylase TaqI, N-terminal domain

结构域编号 domain_id	d2admb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.287 — DNA methylase specificity domain
超家族 Superfamily superfamily	d.287.1 — DNA methylase specificity domain
家族 Family family	d.287.1.1 — TaqI C-terminal domain-like

CATH v4.4 (4 domains)

结构域编号 domain_id	2admA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	2admA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	220 — Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2

结构域编号 domain_id	2admB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	2admB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	220 — Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2

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7. 引用文献 (4)

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晶胞边长 a length_a	130.660 Å
晶胞边长 b length_b	141.830 Å
晶胞边长 c length_c	53.150 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	8

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.2140
R_work r_work	0.2140
R_free r_free	0.2730

fit	/app/data/saxs_computation/ad/2adm/2adm.fit
pddf	/app/data/pr_computation/ad/2adm/2adm.pr.out
profile	/app/data/saxs_computation/ad/2adm/2adm.dat

ADENINE-N6-DNA-METHYLTRANSFERASE TAQI

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution