2ibt

;Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing 2-aminopurine at the target position and an abasic site analog at the target base partner position ;

Method: X-RAY DIFFRACTION D_max: 133.5 Å Quality: REASONABLE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2ibt
沉积日期 deposition_date	2006-09-12
结构标题 title	;Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing 2-aminopurine at the target position and an abasic site analog at the target base partner position ;
关键词 keywords	DNA, DNA methyltransferase, 2-aminopurine, abasic site analog, base flipping, nucleotide flipping, TRANSFERASE-DNA COMPLEX; TRANSFERASE/DNA
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	38.74 Å
回转半径 Rg (电子) rg_electron	39.34 Å
零角强度 I(0) i0	170183000.00
分子量 molecular_weight	103050.0 kDa
排除体积 excluded_volume	127640 Å³
包络体积 envelope_volume	163630 Å³
水化壳体积 shell_volume	37368 Å³
包络直径 envelope_diameter	143.4 Å
壳层 Rg shell_rg	41.15 Å
包络 Rg envelope_rg	38.99 Å
形状 Rg shape_rg	39.34 Å
总 Rg total_rg	39.46 Å
总原子数 total_atoms	7256
残基数 n_residues	820
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	133.5 Å
Rg (实空间) rg_real	39.25 Å
Rg 误差 (实空间) rg_real_error	1.62 Å
I(0) (实空间) i0_real	1.7020e+08
I(0) 误差 (实空间) i0_real_error	3.0060e+06
Rg (倒空间) rg_reciprocal	38.94 Å
I(0) (倒空间) i0_reciprocal	170100000.0000
解质量估计 total_estimate	0.5834
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	29.3 Å
偏度 Skewness skewness	0.497
峰度 Kurtosis kurtosis	-0.557
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	29640000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.634; Stabil: 1.000; Sysdev: 0.132; Positv: 1.000; Valcen: 0.587; Smooth: 0.696

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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	5'-D(GPTPTPCPGP(2PR)PTPGPTPC)-3'
分子量 formula_weight	3051.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	B,E
原子数 atom_count	8297

GTTCGGTGTC

Entity 2 polymer

描述 description	5'-D(GPAPCPAP(3DR)PCPGP(6MA)PAPC)-3'
分子量 formula_weight	2927.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	C,F

GACANCGAAC

Entity 3 polymer

描述 description	Modification methylase 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,D

MGLPPLLSLPSNSAPRSLGRVETPPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREAHGTAYRFVGVEIDPKALDLPPWAEGILADFLLWEPGEAFDLILGNPPYGIVGEASKYPIHVFKAVKDLYKKAFSTWKGKYNLYGAFLEKAVRLLKPGGVLVFVVPATWLVLEDFALLREFLAREGKTSVYYLGEVFPQKKVSAVVIRFQKSGKGLSLWDTQESESGFTPILWAEYPHWEGEIIRFETEETRKLEISGMPLGDLFHIRFAARSPEFKKHPAVRKEPGPGLVPVLTGRNLKPGWVDYEKNHSGLWMPKERAKELRDFYATPHLVVAHTKGTRVVAAWDERAYPWREEFHLLPKEGVRLDPSSLVQWLNSEAMQKHVRTLYRDFVPHLTLRMLERLPVRREYGFHTSPESARNF

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 4 non-polymer

描述 description	5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE
分子量 formula_weight	326.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

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	1041

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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	d2ibta1
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	d2ibta2
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	d2ibtd1
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	d2ibtd2
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	2ibtA01
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	2ibtA02
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	2ibtD01
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	2ibtD02
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 (3)

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晶胞边长 a length_a	59.339 Å
晶胞边长 b length_b	68.699 Å
晶胞边长 c length_c	114.022 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	92.09 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.700 Å
最低分辨率 resolution_low	19.920 Å
R 因子 r_factor	0.1687
R_work r_work	0.1669
R_free r_free	0.2032

fit	/app/data/saxs_computation/ib/2ibt/2ibt.fit
pddf	/app/data/pr_computation/ib/2ibt/2ibt.pr.out
profile	/app/data/saxs_computation/ib/2ibt/2ibt.dat

;Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing 2-aminopurine at the target position and an abasic site analog at the target base partner position ;

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

5. 实体与聚合体信息 (6)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)