SAXSdb — 1ivw

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ivw
沉积日期 deposition_date	2002-03-29
结构标题 title	Crystal structure of copper amine oxidase from Arthrobacter globiformis: Late intermediate in topaquinone biogenesis
关键词 keywords	Oxidoreductase, Copper, Amine oxidase, Biogenesis, TPQ, Freeze-trapp, Intermediate, Quinone cofactor; 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	32.34 Å
回转半径 Rg (电子) rg_electron	31.51 Å
零角强度 I(0) i0	301168000.00
分子量 molecular_weight	137710.0 kDa
排除体积 excluded_volume	171210 Å³
包络体积 envelope_volume	199350 Å³
水化壳体积 shell_volume	51058 Å³
包络直径 envelope_diameter	110.9 Å
壳层 Rg shell_rg	39.92 Å
包络 Rg envelope_rg	31.61 Å
形状 Rg shape_rg	31.48 Å
总 Rg total_rg	32.20 Å
总原子数 total_atoms	9738
残基数 n_residues	1238
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	106.1 Å
Rg (实空间) rg_real	32.26 Å
Rg 误差 (实空间) rg_real_error	0.62 Å
I(0) (实空间) i0_real	3.0120e+08
I(0) 误差 (实空间) i0_real_error	4.3260e+06
Rg (倒空间) rg_reciprocal	32.29 Å
I(0) (倒空间) i0_reciprocal	301200000.0000
解质量估计 total_estimate	0.8750
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	39.0 Å
偏度 Skewness skewness	0.344
峰度 Kurtosis kurtosis	-0.229
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	86760000.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.873

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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
分子量 formula_weight	70752.7 kDa
EC 编号 ec_number	1.4.3.6
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	11046

MTPSTIQTASPFRLASAGEISEVQGILRTAGLLGPEKRIAYLGVLDPARGAGSEAEDRRFRVFIHDVSGARPQEVTVSVTNGTVISAVELDTAATGELPVLEEEFEVVEQLLATDERWLKALAARNLDVSKVRVAPLSAGVFEYAEERGRRILRGLAFVQDFPEDSAWAHPVDGLVAYVDVVSKEVTRVIDTGVFPVPAEHGNYTDPELTGPLRTTQKPISITQPEGPSFTVTGGNHIEWEKWSLDVGFDVREGVVLHNIAFRDGDRLRPIINRASIAEMVVPYGDPSPIRSWQNYFDTGEYLVGQYANSLELGCDCLGDITYLSPVISDAFGNPREIRNGICMHEEDWGILAKHSDLWSGINYTRRNRRMVISFFTTIGNYDYGFYWYLYLDGTIEFEAKATGVVFTSAFPEGGSDNISQLAPGLGAPFHQHIFSARLDMAIDGFTNRVEEEDVVRQTMGPGNERGNAFSRKRTVLTRESEAVREADARTGRTWIISNPESKNRLNEPVGYKLHAHNQPTLLADPGSSIARRAAFATKDLWVTRYADDERYPTGDFVNQHSGGAGLPSYIAQDRDIDGQDIVVWHTFGLTHFPRVEDWPIMPVDTVGFKLRPEGFFDRSPVLDVPANPSQSGSHCHG

来源 Source

来源生物 organism	Arthrobacter globiformis
NCBI 分类编号 ncbi_taxonomy_id	1665
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	COPPER (II) ION
分子量 formula_weight	63.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 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	1308

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1ivwa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.30 — Supersandwich
超家族 Superfamily superfamily	b.30.2 — Amine oxidase catalytic domain
家族 Family family	b.30.2.1 — Amine oxidase catalytic domain

结构域编号 domain_id	d1ivwa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.2 — Amine oxidase N-terminal region
家族 Family family	d.17.2.1 — Amine oxidase N-terminal region

结构域编号 domain_id	d1ivwa3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.2 — Amine oxidase N-terminal region
家族 Family family	d.17.2.1 — Amine oxidase N-terminal region

结构域编号 domain_id	d1ivwb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.30 — Supersandwich
超家族 Superfamily superfamily	b.30.2 — Amine oxidase catalytic domain
家族 Family family	b.30.2.1 — Amine oxidase catalytic domain

结构域编号 domain_id	d1ivwb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.2 — Amine oxidase N-terminal region
家族 Family family	d.17.2.1 — Amine oxidase N-terminal region

结构域编号 domain_id	d1ivwb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.2 — Amine oxidase N-terminal region
家族 Family family	d.17.2.1 — Amine oxidase N-terminal region

CATH v4.4 (6 domains)

结构域编号 domain_id	1ivwA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1ivwA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1ivwA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily	20 — Copper amine oxidase, catalytic domain

结构域编号 domain_id	1ivwB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1ivwB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1ivwB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily	20 — Copper amine oxidase, catalytic domain

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7. 引用文献 (1)

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晶胞边长 a length_a	157.007 Å
晶胞边长 b length_b	62.896 Å
晶胞边长 c length_c	182.834 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	111.82 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	I 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	7.000 Å
R 因子 r_factor	0.2120
R_work r_work	0.2100
R_free r_free	0.2620

fit	/app/data/saxs_computation/iv/1ivw/1ivw.fit
pddf	/app/data/pr_computation/iv/1ivw/1ivw.pr.out
profile	/app/data/saxs_computation/iv/1ivw/1ivw.dat

Crystal structure of copper amine oxidase from Arthrobacter globiformis: Late intermediate in topaquinone biogenesis

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