SAXSdb — 1ixn

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ixn
沉积日期 deposition_date	2002-06-28
结构标题 title	;Enzyme-Substrate Complex of Pyridoxine 5'-Phosphate Synthase ;
关键词 keywords	TIM barrel, enzyme-substrate complex, open-closed transition, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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	36.83 Å
回转半径 Rg (电子) rg_electron	36.07 Å
零角强度 I(0) i0	188179000.00
分子量 molecular_weight	106410.0 kDa
排除体积 excluded_volume	131600 Å³
包络体积 envelope_volume	173580 Å³
水化壳体积 shell_volume	39774 Å³
包络直径 envelope_diameter	110.9 Å
壳层 Rg shell_rg	43.01 Å
包络 Rg envelope_rg	35.05 Å
形状 Rg shape_rg	36.07 Å
总 Rg total_rg	36.53 Å
总原子数 total_atoms	7432
残基数 n_residues	968
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	109.6 Å
Rg (实空间) rg_real	36.61 Å
Rg 误差 (实空间) rg_real_error	1.00 Å
I(0) (实空间) i0_real	1.8820e+08
I(0) 误差 (实空间) i0_real_error	3.2600e+06
Rg (倒空间) rg_reciprocal	36.75 Å
I(0) (倒空间) i0_reciprocal	188200000.0000
解质量估计 total_estimate	0.8791
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	56.1 Å
偏度 Skewness skewness	-0.073
峰度 Kurtosis kurtosis	-0.811
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	51540000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.851; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.880

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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	;Pyridoxine 5'-Phosphate Synthase ;
分子量 formula_weight	26290.1 kDa
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	8149

AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	1-DEOXY-D-XYLULOSE-5-PHOSPHATE
分子量 formula_weight	214.1 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	SN-GLYCEROL-3-PHOSPHATE
分子量 formula_weight	172.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	717

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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	d1ixna_
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.1.24 — Pyridoxine 5'-phosphate synthase
家族 Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

结构域编号 domain_id	d1ixnb_
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.1.24 — Pyridoxine 5'-phosphate synthase
家族 Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

结构域编号 domain_id	d1ixnc_
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.1.24 — Pyridoxine 5'-phosphate synthase
家族 Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

结构域编号 domain_id	d1ixnd_
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.1.24 — Pyridoxine 5'-phosphate synthase
家族 Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

CATH v4.4 (4 domains)

结构域编号 domain_id	1ixnA00
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	70 — Aldolase class I

结构域编号 domain_id	1ixnB00
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	70 — Aldolase class I

结构域编号 domain_id	1ixnC00
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	70 — Aldolase class I

结构域编号 domain_id	1ixnD00
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	70 — Aldolase class I

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7. 引用文献 (3)

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晶胞边长 a length_a	128.900 Å
晶胞边长 b length_b	156.300 Å
晶胞边长 c length_c	127.600 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	32

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1900
R_work r_work	0.1800
R_free r_free	0.2240

fit	/app/data/saxs_computation/ix/1ixn/1ixn.fit
pddf	/app/data/pr_computation/ix/1ixn/1ixn.pr.out
profile	/app/data/saxs_computation/ix/1ixn/1ixn.dat

;Enzyme-Substrate Complex of Pyridoxine 5'-Phosphate Synthase ;

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