1ojd

HUMAN MONOAMINE OXIDASE B IN COMPLEX WITH Lauryldimethylamine-N-oxide (LDAO)

Method: X-RAY DIFFRACTION D_max: 216.9 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	1ojd
沉积日期 deposition_date	2003-07-08
结构标题 title	HUMAN MONOAMINE OXIDASE B IN COMPLEX WITH Lauryldimethylamine-N-oxide (LDAO)
关键词 keywords	OXIDOREDUCTASE, FAD-CONTAINING AMINE OXIDASE, MAOB; 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	68.25 Å
回转半径 Rg (电子) rg_electron	67.94 Å
零角强度 I(0) i0	4410690000.00
分子量 molecular_weight	572000.0 kDa
排除体积 excluded_volume	719300 Å³
包络体积 envelope_volume	1065500 Å³
水化壳体积 shell_volume	127760 Å³
包络直径 envelope_diameter	216.9 Å
壳层 Rg shell_rg	72.84 Å
包络 Rg envelope_rg	64.70 Å
形状 Rg shape_rg	67.94 Å
总 Rg total_rg	68.02 Å
总原子数 total_atoms	40219
残基数 n_residues	4964
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	216.9 Å
Rg (实空间) rg_real	68.00 Å
Rg 误差 (实空间) rg_real_error	1.96 Å
I(0) (实空间) i0_real	4.4110e+09
I(0) 误差 (实空间) i0_real_error	9.2590e+07
Rg (倒空间) rg_reciprocal	69.02 Å
I(0) (倒空间) i0_reciprocal	4419000000.0000
解质量估计 total_estimate	0.8430
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	103.7 Å
偏度 Skewness skewness	-0.100
峰度 Kurtosis kurtosis	-0.616
角度范围 angular_range	— – 0.1150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	138300000.0000
实空间数据点数 n_real_points	24
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.749; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.716

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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 (3)

Entity 1 polymer

描述 description	AMINE OXIDASE [FLAVIN-CONTAINING] B
分子量 formula_weight	58837.7 kDa
EC 编号 ec_number	1.4.3.4
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,L
原子数 atom_count	40219

MSNKCDVVVVGGGISGMAAAKLLHDSGLNVVVLEARDRVGGRTYTLRNQKVKYVDLGGSYVGPTQNRILRLAKELGLETYKVNEVERLIHHVKGKSYPFRGPFPPVWNPITYLDHNNFWRTMDDMGREIPSDAPWKAPLAEEWDNMTMKELLDKLCWTESAKQLATLFVNLCVTAETHEVSALWFLWYVKQCGGTTRIISTTNGGQERKFVGGSGQVSERIMDLLGDRVKLERPVIYIDQTRENVLVETLNHEMYEAKYVISAIPPTLGMKIHFNPPLPMMRNQMITRVPLGSVIKCIVYYKEPFWRKKDYCGTMIIDGEEAPVAYTLDDTKPEGNYAAIMGFILAHKARKLARLTKEERLKKLCELYAKVLGSLEALEPVHYEEKNWCEEQYSGGCYTTYFPPGILTQYGRVLRQPVDRIYFAGTETATHWSGYMEGAVEAGERAAREILHAMGKIPEDEIWQSEPESVDVPAQPITTTFLERHLPSVPGLLRLIGLTTIFSATALGFLAHKRGLLVRV

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	PICHIA PASTORIS

Entity 2 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	10

Entity 3 non-polymer

描述 description	LAURYL DIMETHYLAMINE-N-OXIDE
分子量 formula_weight	229.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

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6. 折叠分类 (SCOP + CATH) 50 domains

SCOP 2.08 (20 domains)

结构域编号 domain_id	d1ojda1
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	d1ojda2
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.16.1.5 — L-aminoacid/polyamine oxidase

结构域编号 domain_id	d1ojdb1
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	d1ojdb2
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.16.1.5 — L-aminoacid/polyamine oxidase

结构域编号 domain_id	d1ojdc1
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	d1ojdc2
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.16.1.5 — L-aminoacid/polyamine oxidase

结构域编号 domain_id	d1ojdd1
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	d1ojdd2
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.16.1.5 — L-aminoacid/polyamine oxidase

结构域编号 domain_id	d1ojde1
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	d1ojde2
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.16.1.5 — L-aminoacid/polyamine oxidase

结构域编号 domain_id	d1ojdf1
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	d1ojdf2
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.16.1.5 — L-aminoacid/polyamine oxidase

结构域编号 domain_id	d1ojdg1
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	d1ojdg2
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.16.1.5 — L-aminoacid/polyamine oxidase

结构域编号 domain_id	d1ojdh1
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	d1ojdh2
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.16.1.5 — L-aminoacid/polyamine oxidase

结构域编号 domain_id	d1ojdi1
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	d1ojdi2
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.16.1.5 — L-aminoacid/polyamine oxidase

结构域编号 domain_id	d1ojdl1
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	d1ojdl2
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.16.1.5 — L-aminoacid/polyamine oxidase

CATH v4.4 (30 domains)

结构域编号 domain_id	1ojdA01
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	1ojdA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ojdA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

结构域编号 domain_id	1ojdB01
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	1ojdB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ojdB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

结构域编号 domain_id	1ojdC01
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	1ojdC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ojdC03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

结构域编号 domain_id	1ojdD01
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	1ojdD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ojdD03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

结构域编号 domain_id	1ojdE01
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	1ojdE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ojdE03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

结构域编号 domain_id	1ojdF01
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	1ojdF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ojdF03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

结构域编号 domain_id	1ojdG01
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	1ojdG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ojdG03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

结构域编号 domain_id	1ojdH01
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	1ojdH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ojdH03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

结构域编号 domain_id	1ojdI01
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	1ojdI02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ojdI03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

结构域编号 domain_id	1ojdL01
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	1ojdL02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ojdL03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

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7. 引用文献 (1)

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晶胞边长 a length_a	108.405 Å
晶胞边长 b length_b	132.431 Å
晶胞边长 c length_c	154.838 Å
晶胞夹角 α angle_alpha	90.14 °
晶胞夹角 β angle_beta	90.45 °
晶胞夹角 γ angle_gamma	114.02 °
晶胞分子数 Z z_pdb	10

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	3.100 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.2523
R_work r_work	0.2522
R_free r_free	0.2604