1xn1

Crystal Structure Of Lumazine Synthase From Brucella Abortus (Orthorhombic Form At 3.05 Angstroms)

Method: X-RAY DIFFRACTION D_max: 102.3 Å Quality: GOOD

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	1xn1
沉积日期 deposition_date	2004-10-04
结构标题 title	Crystal Structure Of Lumazine Synthase From Brucella Abortus (Orthorhombic Form At 3.05 Angstroms)
关键词 keywords	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	33.50 Å
回转半径 Rg (电子) rg_electron	32.76 Å
零角强度 I(0) i0	420364000.00
分子量 molecular_weight	164040.0 kDa
排除体积 excluded_volume	204160 Å³
包络体积 envelope_volume	239360 Å³
水化壳体积 shell_volume	57973 Å³
包络直径 envelope_diameter	107.0 Å
壳层 Rg shell_rg	41.96 Å
包络 Rg envelope_rg	32.51 Å
形状 Rg shape_rg	32.71 Å
总 Rg total_rg	33.55 Å
总原子数 total_atoms	11562
残基数 n_residues	1444
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	102.3 Å
Rg (实空间) rg_real	33.31 Å
Rg 误差 (实空间) rg_real_error	0.52 Å
I(0) (实空间) i0_real	4.2040e+08
I(0) 误差 (实空间) i0_real_error	6.0160e+06
Rg (倒空间) rg_reciprocal	33.43 Å
I(0) (倒空间) i0_reciprocal	420400000.0000
解质量估计 total_estimate	0.9000
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	43.5 Å
偏度 Skewness skewness	0.127
峰度 Kurtosis kurtosis	-0.495
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	210500000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.946

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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	6,7-dimethyl-8-ribityllumazine synthase
分子量 formula_weight	17381.9 kDa
EC 编号 ec_number	2.5.1.78
来源方法 src_method	man
拷贝数 entity_count	10

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J
原子数 atom_count	11578

MNQSCPNKTSFKIAFIQARWHADIVDEARKSFVAELAAKTGGSVEVEIFDVPGAYEIPLHAKTLARTGRYAAIVGAAFVIDGGIYRHDFVATAVINGMMQVQLETEVPVLSVVLTPHHFHESKEHHDFFHAHFKVKGVEAAHAALQIVSERSRIAALV

来源 Source

来源生物 organism	Brucella abortus
NCBI 分类编号 ncbi_taxonomy_id	235
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	24

Entity 3 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 4 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	15

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	16

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d1xn1a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.16 — Lumazine synthase
超家族 Superfamily superfamily	c.16.1 — Lumazine synthase
家族 Family family	c.16.1.1 — Lumazine synthase

结构域编号 domain_id	d1xn1b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.16 — Lumazine synthase
超家族 Superfamily superfamily	c.16.1 — Lumazine synthase
家族 Family family	c.16.1.1 — Lumazine synthase

结构域编号 domain_id	d1xn1c_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.16 — Lumazine synthase
超家族 Superfamily superfamily	c.16.1 — Lumazine synthase
家族 Family family	c.16.1.1 — Lumazine synthase

结构域编号 domain_id	d1xn1d_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.16 — Lumazine synthase
超家族 Superfamily superfamily	c.16.1 — Lumazine synthase
家族 Family family	c.16.1.1 — Lumazine synthase

结构域编号 domain_id	d1xn1e_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.16 — Lumazine synthase
超家族 Superfamily superfamily	c.16.1 — Lumazine synthase
家族 Family family	c.16.1.1 — Lumazine synthase

结构域编号 domain_id	d1xn1f_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.16 — Lumazine synthase
超家族 Superfamily superfamily	c.16.1 — Lumazine synthase
家族 Family family	c.16.1.1 — Lumazine synthase

结构域编号 domain_id	d1xn1g_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.16 — Lumazine synthase
超家族 Superfamily superfamily	c.16.1 — Lumazine synthase
家族 Family family	c.16.1.1 — Lumazine synthase

结构域编号 domain_id	d1xn1h_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.16 — Lumazine synthase
超家族 Superfamily superfamily	c.16.1 — Lumazine synthase
家族 Family family	c.16.1.1 — Lumazine synthase

结构域编号 domain_id	d1xn1i_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.16 — Lumazine synthase
超家族 Superfamily superfamily	c.16.1 — Lumazine synthase
家族 Family family	c.16.1.1 — Lumazine synthase

结构域编号 domain_id	d1xn1j_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.16 — Lumazine synthase
超家族 Superfamily superfamily	c.16.1 — Lumazine synthase
家族 Family family	c.16.1.1 — Lumazine synthase

CATH v4.4 (10 domains)

结构域编号 domain_id	1xn1A00
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	1xn1B00
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	1xn1C00
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	1xn1D00
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	1xn1E00
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	1xn1F00
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	1xn1G00
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	1xn1H00
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	1xn1I00
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	1xn1J00
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	116.554 Å
晶胞边长 b length_b	120.238 Å
晶胞边长 c length_c	159.372 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	40

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	3.050 Å
最低分辨率 resolution_low	56.000 Å
R 因子 r_factor	0.2020
R_work r_work	0.1990
R_free r_free	0.2560

fit	/app/data/saxs_computation/xn/1xn1/1xn1.fit
pddf	/app/data/pr_computation/xn/1xn1/1xn1.pr.out
profile	/app/data/saxs_computation/xn/1xn1/1xn1.dat