SAXSdb — 2gb0

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2gb0
沉积日期 deposition_date	2006-03-09
结构标题 title	Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme
关键词 keywords	FLAVOPROTEIN OXIDASE, 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	30.75 Å
回转半径 Rg (电子) rg_electron	30.20 Å
零角强度 I(0) i0	125274000.00
分子量 molecular_weight	87858.0 kDa
排除体积 excluded_volume	109200 Å³
包络体积 envelope_volume	128620 Å³
水化壳体积 shell_volume	36527 Å³
包络直径 envelope_diameter	113.1 Å
壳层 Rg shell_rg	36.19 Å
包络 Rg envelope_rg	30.25 Å
形状 Rg shape_rg	30.15 Å
总 Rg total_rg	30.84 Å
总原子数 total_atoms	6192
残基数 n_residues	776
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	85.3 Å
Rg (实空间) rg_real	29.45 Å
Rg 误差 (实空间) rg_real_error	0.16 Å
I(0) (实空间) i0_real	1.2010e+08
I(0) 误差 (实空间) i0_real_error	1.3120e+06
Rg (倒空间) rg_reciprocal	30.85 Å
I(0) (倒空间) i0_reciprocal	125300000.0000
解质量估计 total_estimate	0.6812
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	31.2 Å
偏度 Skewness skewness	0.381
峰度 Kurtosis kurtosis	-0.428
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	1.8210
最高正则化参数 α highest_alpha	45460000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.972; Stabil: 0.981; Sysdev: 0.000; Positv: 1.000; Valcen: 0.998; 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	Monomeric sarcosine oxidase
分子量 formula_weight	43101.4 kDa
EC 编号 ec_number	1.5.3.1
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	6928

STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQKTTI

来源 Source

来源生物 organism	Bacillus sp.
NCBI 分类编号 ncbi_taxonomy_id	69000
宿主生物 host_organism	Escherichia coli

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	4

Entity 3 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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	2

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	671

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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	d2gb0a1
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.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d2gb0a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.3 — D-aminoacid oxidase-like

结构域编号 domain_id	d2gb0b1
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.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d2gb0b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.3 — D-aminoacid oxidase-like

CATH v4.4 (4 domains)

结构域编号 domain_id	2gb0A01
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	2gb0A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

结构域编号 domain_id	2gb0B01
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	2gb0B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	72.562 Å
晶胞边长 b length_b	69.555 Å
晶胞边长 c length_c	74.117 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.26 °
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	1.850 Å
最低分辨率 resolution_low	42.530 Å
R 因子 r_factor	—
R_work r_work	0.1650
R_free r_free	0.1980

fit	/app/data/saxs_computation/gb/2gb0/2gb0.fit
pddf	/app/data/pr_computation/gb/2gb0/2gb0.pr.out
profile	/app/data/saxs_computation/gb/2gb0/2gb0.dat

Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme

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