SAXSdb — 2aot

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2aot
沉积日期 deposition_date	2005-08-14
结构标题 title	Histamine Methyltransferase Complexed with the Antihistamine Drug Diphenhydramine
关键词 keywords	CLASSIC METHYLTRANSFERASE FOLD, PROTEIN-DRUG COMPLEX, TRANSFERASE; 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	28.36 Å
回转半径 Rg (电子) rg_electron	27.44 Å
零角强度 I(0) i0	64499100.00
分子量 molecular_weight	63881.0 kDa
排除体积 excluded_volume	80250 Å³
包络体积 envelope_volume	96452 Å³
水化壳体积 shell_volume	29873 Å³
包络直径 envelope_diameter	94.1 Å
壳层 Rg shell_rg	34.11 Å
包络 Rg envelope_rg	27.28 Å
形状 Rg shape_rg	27.46 Å
总 Rg total_rg	28.09 Å
总原子数 total_atoms	4494
残基数 n_residues	572
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	92.8 Å
Rg (实空间) rg_real	28.37 Å
Rg 误差 (实空间) rg_real_error	0.68 Å
I(0) (实空间) i0_real	6.4500e+07
I(0) 误差 (实空间) i0_real_error	9.8760e+05
Rg (倒空间) rg_reciprocal	28.37 Å
I(0) (倒空间) i0_reciprocal	64500000.0000
解质量估计 total_estimate	0.8928
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	91.2 Å
偏度 Skewness skewness	0.306
峰度 Kurtosis kurtosis	-0.498
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	20160000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.921

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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 (5)

Entity 1 polymer

描述 description	Histamine N-methyltransferase
分子量 formula_weight	33365.0 kDa
EC 编号 ec_number	2.1.1.8
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	4931

MASSMRSLFSDHGKYVESFRRFLNHSTEHQCMQEFMDKKLPGIIGRIGDTKSEIKILSIGGGAGEIDLQILSKVQAQYPGVCINNEVVEPSAEQIAKYKELVAKTSNLENVKFAWHKETSSEYQSRMLEKKELQKWDFIHMIQMLYYVKDIPATLKFFHSLLGTNAKMLIIVVSGSSGWDKLWKKYGSRFPQDDLCQYITSDDLTQMLDNLGLKYECYDLLSTMDISDCFIDGNENGDLLWDFLTETCNFNATAPPDLRAELGKDLQEPEFSAKKEGKVLFNNTLSFIVIEA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Histamine N-methyltransferase
分子量 formula_weight	33365.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

MASSMRSLFSDHGKYVESFRRFLNHSTEHQCMQEFMDKKLPGIIGRIGDTKSEIKILSIGGGAGEIDLQILSKVQAQYPGVCINNEVVEPSAEQIAKYKELVAKTSNLENVKFAWHKETSSEYQSRMLEKKELQKWDFIHMIQMLYYVKDIPATLKFFHSLLGTNAKMLIIVVSGSSGWDKLWKKYGSRFPQDDLCQYITSDDLTQMLDNLGLKYECYDLLSTMDISDCFIDGNENGDLLWDFLTETCNFNATAPPDLRAELGKDLQEPEFSAKKEGKVLFNNTLSFIVIEA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	N-[2-(BENZHYDRYLOXY)ETHYL]-N,N-DIMETHYLAMINE
分子量 formula_weight	255.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	S-ADENOSYL-L-HOMOCYSTEINE
分子量 formula_weight	384.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	337

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d2aota_
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.66.1.19 — Histamine methyltransferase

结构域编号 domain_id	d2aotb_
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.66.1.19 — Histamine methyltransferase

CATH v4.4 (2 domains)

结构域编号 domain_id	2aotA00
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	2aotB00
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

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7. 引用文献 (2)

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晶胞边长 a length_a	131.670 Å
晶胞边长 b length_b	131.670 Å
晶胞边长 c length_c	63.750 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	120.00 °
晶胞分子数 Z z_pdb	6

空间群 space_group	P 6
空间群编号 int_tables_number	168
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	35.000 Å
R 因子 r_factor	0.2250
R_work r_work	0.2210
R_free r_free	0.2560

fit	/app/data/saxs_computation/ao/2aot/2aot.fit
pddf	/app/data/pr_computation/ao/2aot/2aot.pr.out
profile	/app/data/saxs_computation/ao/2aot/2aot.dat

Histamine Methyltransferase Complexed with the Antihistamine Drug Diphenhydramine

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 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)