SAXSdb — 1umy

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1umy
沉积日期 deposition_date	2003-09-02
结构标题 title	BHMT from rat liver
关键词 keywords	TRANSFERASE, METHIONINE SYNTHESIS, HOMOCYSTEINE METABOLISM, BETAINE, METHYLTRANSFERASE, ZINC; 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	35.92 Å
回转半径 Rg (电子) rg_electron	35.37 Å
零角强度 I(0) i0	430721000.00
分子量 molecular_weight	167990.0 kDa
排除体积 excluded_volume	209970 Å³
包络体积 envelope_volume	258630 Å³
水化壳体积 shell_volume	58558 Å³
包络直径 envelope_diameter	113.1 Å
壳层 Rg shell_rg	43.53 Å
包络 Rg envelope_rg	34.95 Å
形状 Rg shape_rg	35.33 Å
总 Rg total_rg	36.02 Å
总原子数 total_atoms	11815
残基数 n_residues	1519
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	109.7 Å
Rg (实空间) rg_real	35.77 Å
Rg 误差 (实空间) rg_real_error	0.63 Å
I(0) (实空间) i0_real	4.3070e+08
I(0) 误差 (实空间) i0_real_error	6.3580e+06
Rg (倒空间) rg_reciprocal	35.87 Å
I(0) (倒空间) i0_reciprocal	430800000.0000
解质量估计 total_estimate	0.6710
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	42.4 Å
偏度 Skewness skewness	0.175
峰度 Kurtosis kurtosis	-0.580
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	139200000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 0.028; Positv: 1.000; Valcen: 0.992; Smooth: 0.767

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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 (4)

Entity 1 polymer

描述 description	Betaine--homocysteine S-methyltransferase 1
分子量 formula_weight	45055.4 kDa
EC 编号 ec_number	2.1.1.5
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	12353

MAPIAGKKAKRGILERLNAGEVVIGDGGFVFALEKRGYVKAGPWTPEAAVEHPEAVRQLHREFLRAGSNVMQTFTFYASEDKLENRGNYVAEKISGQKVNEAACDIARQVADEGDALVAGGVSQTPSYLSCKSETEVKKIFHQQLEVFMKKNVDFLIAEYFEHVEEAVWAVEALKTSGKPIAATMCIGPEGDLHGVSPGECAVRLVKAGAAIVGVNCHFDPSTSLQTIKLMKEGLEAARLKAYLMSQPLAYHTPDCGKQGFIDLPEFPFGLEPRVATRWDIQKYAREAYNLGVRYIGGCCGFEPYHIRAIAEELAPERGFLPPASEKHGSWGSGLDMHTKPWIRARARKEYWQNLRIASGRPYNPSMSKPDAWGVTKGAAELMQQKEATTEQQLRALFEKQKFKSAQ

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	BETA-MERCAPTOETHANOL
分子量 formula_weight	78.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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	538

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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	d1umya_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.26 — Homocysteine S-methyltransferase
家族 Family family	c.1.26.1 — Homocysteine S-methyltransferase

结构域编号 domain_id	d1umyb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.26 — Homocysteine S-methyltransferase
家族 Family family	c.1.26.1 — Homocysteine S-methyltransferase

结构域编号 domain_id	d1umyc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.26 — Homocysteine S-methyltransferase
家族 Family family	c.1.26.1 — Homocysteine S-methyltransferase

结构域编号 domain_id	d1umyd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.26 — Homocysteine S-methyltransferase
家族 Family family	c.1.26.1 — Homocysteine S-methyltransferase

CATH v4.4 (4 domains)

结构域编号 domain_id	1umyA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	330 — Homocysteine-binding-like domain

结构域编号 domain_id	1umyB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	330 — Homocysteine-binding-like domain

结构域编号 domain_id	1umyC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	330 — Homocysteine-binding-like domain

结构域编号 domain_id	1umyD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	330 — Homocysteine-binding-like domain

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7. 引用文献 (3)

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晶胞边长 a length_a	57.830 Å
晶胞边长 b length_b	149.270 Å
晶胞边长 c length_c	96.250 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	92.92 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.500 Å
最低分辨率 resolution_low	48.400 Å
R 因子 r_factor	0.2530
R_work r_work	0.2530
R_free r_free	0.2910

fit	/app/data/saxs_computation/um/1umy/1umy.fit
pddf	/app/data/pr_computation/um/1umy/1umy.pr.out
profile	/app/data/saxs_computation/um/1umy/1umy.dat

BHMT from rat liver

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