SAXSdb — 1knp

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1knp
沉积日期 deposition_date	2001-12-19
结构标题 title	E. coli L-aspartate oxidase: mutant R386L in complex with succinate
关键词 keywords	fumarate reductase family of oxidoreductases, OXIDOREDUCTASE; OXIDOREDUCTASE
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	23.77 Å
回转半径 Rg (电子) rg_electron	22.71 Å
零角强度 I(0) i0	62291400.00
分子量 molecular_weight	59869.0 kDa
排除体积 excluded_volume	74171 Å³
包络体积 envelope_volume	85373 Å³
水化壳体积 shell_volume	30052 Å³
包络直径 envelope_diameter	76.8 Å
壳层 Rg shell_rg	31.01 Å
包络 Rg envelope_rg	23.14 Å
形状 Rg shape_rg	22.73 Å
总 Rg total_rg	23.51 Å
总原子数 total_atoms	4212
残基数 n_residues	529
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	74.9 Å
Rg (实空间) rg_real	23.63 Å
Rg 误差 (实空间) rg_real_error	0.40 Å
I(0) (实空间) i0_real	6.2290e+07
I(0) 误差 (实空间) i0_real_error	7.8640e+05
Rg (倒空间) rg_reciprocal	23.67 Å
I(0) (倒空间) i0_reciprocal	62290000.0000
解质量估计 total_estimate	0.8179
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	29.2 Å
偏度 Skewness skewness	0.207
峰度 Kurtosis kurtosis	-0.414
角度范围 angular_range	— – 0.3350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	19800000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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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	L-aspartate oxidase
分子量 formula_weight	60386.3 kDa
EC 编号 ec_number	1.4.3.16
突变 mutation	R386L
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	4232

MNTLPEHSCDVLIIGSGAAGLSLALRLADQHQVIVLSKGPVTEGSTFYAQGGIAAVFDETDSIDSHVEDTLIAGAGICDRHAVEFVASNARSCVQWLIDQGVLFDTHIQPNGEESYHLTREGGHSHRRILHAADATGREVETTLVSKALNHPNIRVLERTNAVDLIVSDKIGLPGTRRVVGAWVWNRNKETVETCHAKAVVLATGGASKVYQYTTNPDISSGDGIAMAWRAGCRVANLEFNQFHPTALYHPQARNFLLTEALRGEGAYLKRPDGTRFMPDFDERGELAPRDIVARAIDHEMKRLGADCMFLDISHKPADFIRQHFPMIYEKLLGLGIDLTQEPVPIVPAAHYTCGGVMVDDHGRTDVEGLYAIGEVSYTGLHGANLMASNSLLECLVYGWSAAEDITRRMPYAHDISTLPPWDESRVENPDERVVIQHNWHELRLFMWDYVGIVRTTKRLERALRRITMLQQEIDEYYAHFRVSNNLLELRNLVQVAELIVRCAMMRKESRGLHFTLDYPELLTHSGPSILSPGNHYINR

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 BL21

Entity 2 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	1

Entity 3 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	SUCCINIC ACID
分子量 formula_weight	118.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	20

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1knpa1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.7 — Spectrin repeat-like
超家族 Superfamily superfamily	a.7.3 — Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain
家族 Family family	a.7.3.1 — Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain

结构域编号 domain_id	d1knpa2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.4 — Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain

结构域编号 domain_id	d1knpa3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.168 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
超家族 Superfamily superfamily	d.168.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
家族 Family family	d.168.1.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

CATH v4.4 (3 domains)

结构域编号 domain_id	1knpA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1knpA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	700 — Flavocytochrome C3; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

结构域编号 domain_id	1knpA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	100 — Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	72.540 Å
晶胞边长 b length_b	72.540 Å
晶胞边长 c length_c	309.120 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	8

空间群 space_group	P 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.2325
R_work r_work	0.2300
R_free r_free	0.2808

fit	/app/data/saxs_computation/kn/1knp/1knp.fit
pddf	/app/data/pr_computation/kn/1knp/1knp.pr.out
profile	/app/data/saxs_computation/kn/1knp/1knp.dat

E. coli L-aspartate oxidase: mutant R386L in complex with succinate

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