1w19

;Lumazine Synthase from Mycobacterium tuberculosis bound to 3-(1,3,7- trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)propane 1-phosphate ;

Method: X-RAY DIFFRACTION D_max: 80.9 Å Quality: EXCELLENT

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	1w19
沉积日期 deposition_date	2004-06-03
结构标题 title	;Lumazine Synthase from Mycobacterium tuberculosis bound to 3-(1,3,7- trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)propane 1-phosphate ;
关键词 keywords	TRANSFERASE, RIBOFLAVIN BIOSYNTHESIS, LUMAZINE SYNTHASE, INHIBITOR BINDING; 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	26.75 Å
回转半径 Rg (电子) rg_electron	25.61 Å
零角强度 I(0) i0	107985000.00
分子量 molecular_weight	79331.0 kDa
排除体积 excluded_volume	98451 Å³
包络体积 envelope_volume	116050 Å³
水化壳体积 shell_volume	35851 Å³
包络直径 envelope_diameter	81.8 Å
壳层 Rg shell_rg	34.54 Å
包络 Rg envelope_rg	25.86 Å
形状 Rg shape_rg	25.57 Å
总 Rg total_rg	26.63 Å
总原子数 total_atoms	5520
残基数 n_residues	733
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	80.9 Å
Rg (实空间) rg_real	26.57 Å
Rg 误差 (实空间) rg_real_error	0.34 Å
I(0) (实空间) i0_real	1.0800e+08
I(0) 误差 (实空间) i0_real_error	1.4030e+06
Rg (倒空间) rg_reciprocal	26.62 Å
I(0) (倒空间) i0_reciprocal	108000000.0000
解质量估计 total_estimate	0.9085
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	34.3 Å
偏度 Skewness skewness	0.129
峰度 Kurtosis kurtosis	-0.526
角度范围 angular_range	— – 0.2950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	26800000.0000
实空间数据点数 n_real_points	60
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.985

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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 (11)

Entity 1 polymer

描述 description	6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
分子量 formula_weight	16387.6 kDa
EC 编号 ec_number	2.5.1.9
来源方法 src_method	man
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E
原子数 atom_count	6151

MKGGAGVPDLPSLDASGVRLAIVASSWHGKICDALLDGARKVAAGCGLDDPTVVRVLGAIEIPVVAQELARNHDAVVALGVVIRGQTPHFDYVCDAVTQGLTRVSLDSSTPIANGVLTTNTEEQALDRAGLPTSAEDKGAQATVAALATALTLRELRAHS

来源 Source

来源生物 organism	MYCOBACTERIUM TUBERCULOSIS
NCBI 分类编号 ncbi_taxonomy_id	1773
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	ACETIC ACID
分子量 formula_weight	60.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 3 non-polymer

描述 description	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
分子量 formula_weight	154.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	3-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE
分子量 formula_weight	440.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	13

Entity 6 non-polymer

描述 description	3-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE
分子量 formula_weight	440.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
分子量 formula_weight	154.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 8 non-polymer

描述 description	3-{2,6,8-TRIOXO-9-[(2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE
分子量 formula_weight	440.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 9 non-polymer

描述 description	3-{2,6,8-TRIOXO-9-[(2R,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE
分子量 formula_weight	440.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 10 non-polymer

描述 description	(4S,5S)-1,2-DITHIANE-4,5-DIOL
分子量 formula_weight	152.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 11 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	631

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6. 折叠分类 (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

结构域编号 domain_id	1w19A00
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	960 — Lumazine/riboflavin synthase

结构域编号 domain_id	1w19B00
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	960 — Lumazine/riboflavin synthase

结构域编号 domain_id	1w19C00
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	960 — Lumazine/riboflavin synthase

结构域编号 domain_id	1w19D00
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	960 — Lumazine/riboflavin synthase

结构域编号 domain_id	1w19E00
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	960 — Lumazine/riboflavin synthase

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7. 引用文献 (1)

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晶胞边长 a length_a	131.267 Å
晶胞边长 b length_b	80.688 Å
晶胞边长 c length_c	86.188 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	120.29 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	20

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	19.540 Å
R 因子 r_factor	0.1510
R_work r_work	0.1490
R_free r_free	0.1940

fit	/app/data/saxs_computation/w1/1w19/1w19.fit
pddf	/app/data/pr_computation/w1/1w19/1w19.pr.out
profile	/app/data/saxs_computation/w1/1w19/1w19.dat