SAXSdb — 1q85

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1q85
沉积日期 deposition_date	2003-08-20
结构标题 title	Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima (Cd2+ complex, Se-Met)
关键词 keywords	homocysteine, methionine, folate, cobalamin, vitamin b12, 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	44.93 Å
回转半径 Rg (电子) rg_electron	45.23 Å
零角强度 I(0) i0	224182000.00
分子量 molecular_weight	125760.0 kDa
排除体积 excluded_volume	158470 Å³
包络体积 envelope_volume	202630 Å³
水化壳体积 shell_volume	41906 Å³
包络直径 envelope_diameter	158.2 Å
壳层 Rg shell_rg	43.04 Å
包络 Rg envelope_rg	44.90 Å
形状 Rg shape_rg	45.20 Å
总 Rg total_rg	45.21 Å
总原子数 total_atoms	8779
残基数 n_residues	1089
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	147.1 Å
Rg (实空间) rg_real	45.66 Å
Rg 误差 (实空间) rg_real_error	1.62 Å
I(0) (实空间) i0_real	2.2420e+08
I(0) 误差 (实空间) i0_real_error	4.3640e+06
Rg (倒空间) rg_reciprocal	44.93 Å
I(0) (倒空间) i0_reciprocal	224000000.0000
解质量估计 total_estimate	0.6948
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	29.4 Å
偏度 Skewness skewness	0.565
峰度 Kurtosis kurtosis	-0.542
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	31120000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.557; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.342; Smooth: 0.016

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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	5-methyltetrahydrofolate S-homocysteine methyltransferase
分子量 formula_weight	64102.1 kDa
EC 编号 ec_number	2.1.1.13
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	8923

MRNRREVSKLLSERVLLLDGAYGTEFMKYGYDDLPEELNIKAPDVVLKVHRSYIESGSDVILTNTFGATRMKLRKHGLEDKLDPIVRNAVRIARRAAGEKLVFGDIGPTGELPYPLGSTLFEEFYENFRETVEIMVEEGVDGIIFETFSDILELKAAVLAAREVSRDVFLIAHMTFDEKGRSLTGTDPANFAITFDELDIDALGINCSLGPEEILPIFQELSQYTDKFLVVEPNAGKPIVENGKTVYPLKPHDFAVHIDSYYELGVNIFGGCCGTTPEHVKLFRKVLGNRKPLQRKKKRIFAVSSPSKLVTFDHFVVIGERINPAGRKKLWAEMQKGNEEIVIKEAKTQVEKGAEVLDVNFGIESQIDVRYVEKIVQTLPYVSNVPLSLDIQNVDLTERALRAYPGRSLFNSAKVDEEELEMKINLLKKYGGTLIVLLMGKDVPKSFEERKEYFEKALKILERHDFSDRVIFDPGVLPLGAEGKPVEVLKTIEFISSKGFNTTVGLSNLSFGLPDRSYYNTAFLVLGISKGLSSAIMNPLDETLMKTLNATLVILEKKELPRAEVK

来源 Source

来源生物 organism	Thermotoga maritima
NCBI 分类编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	CADMIUM ION
分子量 formula_weight	112.4 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	144

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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	d1q85a1
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.1.21 — Dihydropteroate synthetase-like
家族 Family family	c.1.21.2 — Methyltetrahydrofolate-utiluzing methyltransferases

结构域编号 domain_id	d1q85a2
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	d1q85b1
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.1.21 — Dihydropteroate synthetase-like
家族 Family family	c.1.21.2 — Methyltetrahydrofolate-utiluzing methyltransferases

结构域编号 domain_id	d1q85b2
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	1q85A01
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	1q85A02
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	20 — Dihydropteroate synthase-like

结构域编号 domain_id	1q85B01
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	1q85B02
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	20 — Dihydropteroate synthase-like

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7. 引用文献 (1)

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晶胞边长 a length_a	60.300 Å
晶胞边长 b length_b	86.170 Å
晶胞边长 c length_c	125.880 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	100.39 °
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	2.000 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2680
R_work r_work	0.2430
R_free r_free	0.2830

fit	/app/data/saxs_computation/q8/1q85/1q85.fit
pddf	/app/data/pr_computation/q8/1q85/1q85.pr.out
profile	/app/data/saxs_computation/q8/1q85/1q85.dat

Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima (Cd2+ complex, Se-Met)

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution