SAXSdb — 1h3i

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1h3i
沉积日期 deposition_date	2002-09-04
结构标题 title	Crystal structure of the Histone Methyltransferase SET7/9
关键词 keywords	TRANSFERASE, METHYLTRANSFERASE; TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	27.74 Å
回转半径 Rg (电子) rg_electron	26.66 Å
零角强度 I(0) i0	73377100.00
分子量 molecular_weight	65107.0 kDa
排除体积 excluded_volume	80556 Å³
包络体积 envelope_volume	103770 Å³
水化壳体积 shell_volume	31683 Å³
包络直径 envelope_diameter	86.6 Å
壳层 Rg shell_rg	34.66 Å
包络 Rg envelope_rg	26.27 Å
形状 Rg shape_rg	26.63 Å
总 Rg total_rg	27.61 Å
总原子数 total_atoms	4591
残基数 n_residues	586
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	82.6 Å
Rg (实空间) rg_real	27.57 Å
Rg 误差 (实空间) rg_real_error	0.40 Å
I(0) (实空间) i0_real	7.3380e+07
I(0) 误差 (实空间) i0_real_error	9.5980e+05
Rg (倒空间) rg_reciprocal	27.62 Å
I(0) (倒空间) i0_reciprocal	73380000.0000
解质量估计 total_estimate	0.9149
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	34.8 Å
偏度 Skewness skewness	0.072
峰度 Kurtosis kurtosis	-0.693
角度范围 angular_range	— – 0.2850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	12750000.0000
实空间数据点数 n_real_points	58
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.978; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.957

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	HISTONE H3 LYSINE 4 SPECIFIC METHYLTRANSFERASE
分子量 formula_weight	32571.9 kDa
EC 编号 ec_number	2.1.1.43
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	4935

FFFDGSTLEGYYVDDALQGQGVYTYEDGGVLQGTYVDGELNGPAQEYDTDGRLIFKGQYKDNIRHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSPPGK

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 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 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	344

▼

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1h3ia1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.76 — open-sided beta-meander
超家族 Superfamily superfamily	b.76.2 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
家族 Family family	b.76.2.1 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

结构域编号 domain_id	d1h3ia2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.85 — beta-clip
超家族 Superfamily superfamily	b.85.7 — SET domain
家族 Family family	b.85.7.1 — Histone lysine methyltransferases

结构域编号 domain_id	d1h3ib1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.76 — open-sided beta-meander
超家族 Superfamily superfamily	b.76.2 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
家族 Family family	b.76.2.1 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

结构域编号 domain_id	d1h3ib2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.85 — beta-clip
超家族 Superfamily superfamily	b.85.7 — SET domain
家族 Family family	b.85.7.1 — Histone lysine methyltransferases

CATH v4.4 (4 domains)

结构域编号 domain_id	1h3iA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	110 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
同源超家族 H-superfamily homologous superfamily	10 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

结构域编号 domain_id	1h3iA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	270 — Beta-clip-like
同源超家族 H-superfamily homologous superfamily	10 — SET domain

结构域编号 domain_id	1h3iB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	110 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
同源超家族 H-superfamily homologous superfamily	10 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

结构域编号 domain_id	1h3iB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	270 — Beta-clip-like
同源超家族 H-superfamily homologous superfamily	10 — SET domain

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	66.090 Å
晶胞边长 b length_b	82.830 Å
晶胞边长 c length_c	116.150 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 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2120
R_work r_work	0.2100
R_free r_free	0.2550

fit	/app/data/saxs_computation/h3/1h3i/1h3i.fit
pddf	/app/data/pr_computation/h3/1h3i/1h3i.pr.out
profile	/app/data/saxs_computation/h3/1h3i/1h3i.dat

Crystal structure of the Histone Methyltransferase SET7/9

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